As the scientific groundwork for the spatial sustainable development planning and management, spatial development function regionalization can provide regional division of different development directions and potentials based on the regional disparities of the natural, social, economic and environmental characteristics. After looking back and comparing the theory, principle, index, method and function area among natural regionalization, agricultural regionalization, ecological regionalization and economic regionalization, etc., this paper puts forward the concept and characteristics of the spatial development function regionalization by equilibrium between natural and economic systems, integration of spatial development and spatial governess, harmony of population, economic resource and environment. Then, it focuses the discussion on the regionalization methods, types, and indices. Using the method of classification matrix integrated by the economic development value and ecological conservation value, several functional regional types, namely feasible development area, limitary development area, moderate conservation area, prohibited exploiting area and elasticity gray area, can be divided and marked out according to the various combinations of the economic development value and ecological conservation value. Furthermore, the paper probes the evaluation indices system as well as applies the evaluation methods along with classification clustering and matrix both to the economic development value and ecological conservation value of each regional unit. Finally, the paper takes waterfront along the Yangtze River in Nantong city, Jiangsu Province as a case study for the development function regionalization of waterfront. The economic development value of waterfront (i.e. the harbor construction value) has been evaluated by the indices of waterfront depth, stability, river breadth before waterfront and land width behind waterfront and then three value levels have been divided. Meanwhile the ecological protection value can be appraised by judging that whether the region cell has domestic water source, ecological isolated area, tourism area, historic relics or the possibility of frequent occurrence of geological hazards and then three value levels have also been divided. By the classification matrix of the economic development value and the ecological conservation value of 14 appraising units, these units are separated into five development function types or waterfront can be divided into feasible development waterfront, limitary development waterfront, moderate conservation waterfront, prohibited development waterfront and gray elasticity waterfront. According to the classification result, some valuable advices about waterfront development and adjustment can be provided.