A comprehensive investigation was carried out at 16 stations in the Yangtze River hypoxia area and the adjacent East China Sea in August, 2011. The hypoxia area located in the bottom with an area of about 1 028 km² and the lowest dissolved oxygen concentration was measured to be 1.85 mg/L. Total 82 water samples of phytoplankton were collected in this sea area and were analyzed by Utermhl method. 82 phytoplankton species was indentifed and belonged to 37 genera of 4 classes. Diatoms were the dominant population in the area, and Skeletonema costatum was the dominant species. The phytoplankton ecological type belonged to temperate zone nearshore algae and euryhaline algae. Cell abundance of phytoplankton ranged from 6.31×10³ cells/L to 7.80×10⁶ cells/L, and the average cell abundance was about 7.59×10⁵ cells/L. The phytoplankton cell abundance reduced rapidly from water surface layer to bottom. It was found that the cell abundance, diversity index, evenness index was the core low oxygen area > not core low oxygen area > the non low oxygen area in turn, but there were no significant difference for phytoplankton species. And the phytoplankton cell abundance had the positive relation with temperature, COD, chlorophyll a,and nitrate concentration, but the negtive relation with salinity. And there was no significant effect between the phytoplankton cell abundance and the dissolved oxygen content, suspended matter content, phosphlate and ammonia nitrogen concentration.