The relationship between biological indicators of water body and hydrodynamic parameters of river is one of the important research subject of aquatic ecosystem. The paper set 31 diatom sampling points at Liujiang river to explore the community structure of surface sediment diatoms under different hydrodynamic conditions and focused on relationship between diatoms and hydrological variables such as water depth, velocity and flow. The diatoms found in the study area are 264 kinds of 2 classes 38.Through layered diagrams and sequence analysis, the flow rate is the most important hydrodynamic condition that influences diatom community distribution, followed by the Reynolds number. The relation between the size of Reynolds number and abundance of planktonic species is close, but the influence of Reynolds number on diatom species is also uncertain. Planktonic species such as Melosira and Cyclotella more easily appear in the river than in the creek, while artificial dam changes the hydrodynamic conditions and has impact on the distribution of algae, especially in the downstream reservoir and other more extreme turbulence conditions ,the abundance of cymbella and fragilaria show a growth trend.