In order to know more about the resources condition of phytoplankton in anhui-jiangsu reach of Yangtze river and provide more scientific warrant for evaluating eco-environment, exploiting and utilizing resources in anhui-jiangsu reach of Yangtze river, the investigation was conducted. The structure of phytoplankton was analyzed according to species composition, quantity, biomass and Mcnaughton dominance index, and the spatial distribution characteristic of phytoplankton was analyzed according to the clustering analytical method simultaneously. The results showed that there were 5 classes, including 27 species of phytoplankton had been recorded in the anhui-jiangsu reach of Yangtze river in autumn. Among them, Bacillariophyta was the predominant species, which had 16 species, accounted for 59.3% of the total species. Chlorophyta was recorded 6 species, accounted for 22.2%. Cyanophyta, Cryptophyta and Euglenophyta were recorded 2, 2, 1 species each and accounted for 7.4%, 7.4%, 3.7% respectively. The predominant species of phytoplankton in the anhui-jiangsu reach of Yangtze river in autumn were Fragilaria crotonensis, Melosira italica, Navicula cryptocephala, Cyclotella and Chroomonas acuta. The phytoplankton abundance in the anhui-jiangsu reach of Yangtze river in autumn ranged from 5.68×104 cells/L to 7.08×104 cells/L, with the average of 6.01×104 cells/L, and the phytoplankton biomass ranged from 30.43 μg/L to 34.73 μg/L, with the average of 32.46 μg/L. The number of phytoplankton species decreased and the phytoplankton abundance and biomass increased compared with the results of previous studies, which meant that the water quality in the jiangsu reach of Yangtze river had deteriorated. However, Bacillariophyta was still the main predominant species and the phytoplankton community structure had not changed significantly compared with the results of previous studies, which meant that the water quality in the jiangsu reach of Yangtze river had not deteriorated seriously. The results of similarity clustering of phytoplankton community indicated that the phytoplankton community at nanjing, wuhu and jiangyin were similar and the phytoplankton community at tongling was similar to that at anqing.