The frequencies occurring alga blooms in the backwater areas of tributaries of the Three Gorges Reservoir (TGR) have been a hot eco-environmental problem in this region. A gradient analysis based on the canonical correspondence analysis (CCA) was put forward to investigate the potential relationship between environmental factors and phytoplankton assemblages. It was found that the CCA model is effective and possesses a higher obviousness. Seasonal operation of the reservoir forms distinct existence conditions for phytoplankton assemblages. In summer season, the water body of surface is characterized by discharge change and many suspended particles, and it makes some phytoplanktons(e.g. syna etc.) form relative existence superiority. In the winter season, the rise of the water level in the TGR makes the habitat like deep lakes, the phytoplankton that prevails in the cold water and possesses moving function becomes the dominance species.