As workers leave the countryside in the hope of better pay, the communities they leave behind face increasing poverty

To understand just how poor rural Guizhou is, you can look at the statistics. Or you can look at the children in Qixin village.

Zhao Ai is nine, but is so short he appears three years younger. He eats nothing between leaving home at 6.30am – for a two-hour trek down the mountain to Ruiyuan primary school – and returning at 5pm.

Last year, Shanghai took the top spot in the Organisation for Economic Co-operation and Development (OECD)'s international rankings for reading, maths and science in state schools. Meanwhile, at Zhao's primary, the big educational challenge is "no food", says headteacher Xu Zuhua. Malnutrition stunts her pupils' growth and hampers their concentration.

There is no better illustration of the growing gulf between cities and the countryside as China transforms itself from a rural to an urban nation. Between 1990 and 2009, China slashed its numbers of rural poor from 85 million to 35.97 million, thanks in large part to the wages sent home by migrant workers. The government hopes further urbanisation will lift children like Zhao out of poverty.

Yet many fear that two Chinas are emerging, with the countryside falling ever further behind.

"Even though we are developing, it feels like urban areas are running while we are strolling," says Zhou Liude, who oversees Ruiyuan and nearby schools.

For every one yuan of a rural resident's income, a city-dweller enjoys 3.23 yuan in disposable income – and that may significantly understate the gap. Include the extra services and benefits enjoyed by urbanites, such as subsidised housing, and "many observers believe that the ratio would easily be in the range of four to five and is arguably among the highest in the world," says professor Kam Wing Chan, an expert on migrants at the University of Washington.

"China's incomes are increasingly polarised. This large income gap is definitely a contributor in the background to the more frequent and violent protests and unrest in the last few months."

Even farmers who reach the cities as migrant workers are in effect second-class citizens, because China's hukou – household registration – system classifies people as urban or rural and allocates rights to services accordingly. One Chinese academic has described the result as "counterfeit urbanisation": cities full of people who cannot enjoy much of city life.

The government has sought to invest in rural areas, and the benefits of growth are spreading. In the towns around Qixin you see stores with gleaming yellow motorbikes and adverts for 3G and coffee.

But these remain unimaginable luxuries for families like Zhao's, who survive on basic farming and wages sent home by relatives working in cities. Their poverty is disguised by development: the further away from the road people live, the poorer they are – and the worse their children's grades – says Ruiyuan's headteacher.

Education has always been the great hope for China's poor. Villagers built Ruiyuan themselves to improve their children's opportunities. But rural scholars lag their peers from the start.

Zhao Ai's father died in a mudslide; his mother is a migrant labourer hundreds of miles away. He is one of China's 50 million "left behind" children, raised by grandparents because the hukou system makes family migration difficult. They have inferior educational results and more behavioural problems than the average child. Relatives can be unable or unwilling to care for them properly; sometimes, they are carers for sick and ageing grandparents. With few adults around, they must help with household chores and farming before they can turn to homework.

Zhao Ai is lucky; his family make up in warmth what they lack in income. But he is an anxious child, noticeably quieter than his boisterous schoolmates. He struggles on the steep climb back home, a punishing scramble through woods and fields, on an empty stomach.

Education officials want to build a boarding school and have even found a company willing to donate 400,000 yuan (about £40,000) – but would need three times that to pipe water to the site. So for the foreseeable future, Zhao Ai and his friends are stuck with their long journeys and school days in an ageing, cracking building with no running water or heating. Finding suitable staff is hard because few young graduates want to live somewhere so remote. English is compulsory, but Ruiyuan has nobody capable of teaching it.

Experts say the disparity between rural and urban educational standards is one reason why the proportion of rural students in universities – particularly the top ones – is falling rapidly. According to Chinese media, pupils from the countryside made up 62% of those sitting national college entrance exams last year, but only 17% of those entering the elite Tsinghua University.

In recent years, Chinese leaders have sought to give rural areas more help. Official statistics suggest the income gap may have closed slightly within the last year, though experts suspect this reflects sampling changes.

Li Keqiang, who is expected to become premier next year, has suggested urbanisation could "pull up" the countryside as a smaller number of farmers consolidate land, leading to increased productivity – though much farmland is being lost to development. Yet the best prospect for most farmers remains a move to the cities.

Wang Fang and her husband, Chen Shuangfu, arrived in the provincial capital, Guiyang, 10 years ago, with just 10 yuan in their pockets. Their hard, unappealing work – collecting and sorting rubbish for recycling – earns them as much as 20,000 yuan a year, compared with their 1,000 yuan income back home. But their rural hukou means they are not entitled to many services – and, since the hukou is inherited, neither are their sons. Schools do not receive extra funding for migrant pupils; many claim they are full, or charge hefty illicit fees. The couple have spent 50,000 yuan since their sons reached school age in "donations" to get them into a public school and illicit extra fees.

"I can't read or write; I can't even speak standard Mandarin well. We don't want our children to be like us," says Chen. Migrant workers build China's cities, clean their homes and clear their rubbish – but other residents "call us beggars and use dirty words," added Wang.

That might not have mattered so much to an earlier generation of workers, who planned to return to their villages in retirement. But many younger migrants have little experience of farming, and believe their futures lie in towns.

"[Urbanisation] is better than an economy without growth. But when you grow, you also have to provide services to [migrants] and not only use them as cheap labour … You need children to move with their parents to cities and you need services for the left-behind elderly," warns Tao Ran, an expert on rural affairs at Renmin University.

There are promising pilot projects that attempt to tackle the urban-rural gulf: improving education for poorer children; increasing integration. Cities such as Chongqing and Guangdong have been experimenting with limited hukou reform.

But such programmes are often tightly restricted and cover workers who have moved from country to town within a province. In many cases migrants have been wary of switching registration, fearing the compensation for lost land and home is insufficient to establish them in the city.

Chan, of the University of Washington, said reforms needed to go deeper and to involve Beijing.

"Hukou reform has to be gradual, but it has to tackle the core of the issue," he says. "The core issue, for example, in Guangdong, is to gradually accept migrant workers from outside the province – the majority of the migrant workers – as equals."

Wholesale hukou reform is an alarming prospect for officials, raising the spectre of an expensive and uncontrollable surge to the cities. But the alternative is an unbridgeable gap between town and country – with children such as Zhao Ai stranded in poverty as his urban peers romp ahead.

Additional research by Han Cheng