Background and Aims Root system is the main organ for absorbing water and nutrients, and the first contact to sense soil and environmental stresses. Plant root morphology and internal physiological characteristics are affected by soil moisture content, leading to differences in the rate of plant water uptake. Methods The common reeds (Phragmites australis) were treated for 45 days at four different soil moisture content. Harvesting starts after 30 days of the treatment and the morphological characteristics, anatomical characteristics and hydraulic conductivity of the common reed root system are measured using pressure chambers and paraffin sections And common reed root transcriptomic profiles were assessed using next-generation RNA sequencing. Results The root system shrinks morphologically and anatomically during a drought. Decrease in soil moisture significantly reduced hydraulic conductivity of both the whole and single root of the common reed. RNA-seq results implicated abscisic acid (ABA) related genes in the regulation of hydraulic conductivity, with the expression profiles of ABA1, 9-cis-epoxycarotenoid dioxygenase (NCED), ABA2, and abscisic-aldehyde oxidase 3(AAO3) showing an overall decreasing trend as drought conditions intensified. Plasma membrane intrinsic proteins (PIPs) contents varied under different soil water treatments with up-regulated expression under 60% field capacity treatment indicating that PIP genes were regulated by drought stress to some extent. Conclusion Soil moisture contents significantly influenced root morphological, anatomical characteristics, and induced the expression of root-sourced ABA and aquaporins in common reed, which in turn altered root hydraulic conductivity.