Abstract: To explore the pattern of spatialvariations in phytoplankton community structure and the characteristics of floracomposition in the main stem of the Yangtze River basin，we set 74 sampling sectionsat five researchregions(i.e.，headwater region，Jinsha Riverregion，Three Gorge reservoir，middle and lower reaches of the Yangtze River) in the main stem to conduct the field survey on phytoplankton in July-September of 2019. A total of 112 species，belonging to 6 phyla in 53 genera，were identified during the survey. Bacillariophyta was the dominant taxa except the lower reach area. Diatoms were predominant at five research areas，e.g.，Synedra acus，Diatoma vulgare，Melosira granulata var. Angustissima. The mean density and biomass of phytoplankton throughout the main stem were 1.29×106 cells/L and 1.34 mg/L，respectively. Statisticallysignificant differences were foundin thespecies composition，Diatom Quotient and the diversity indices among five research areas. Specifically，the phytoplankton species in the headwater region were extremely dissimilar to those at other regions. The Diatom Quotient atthe lower reaches were significantly higher than those in other regions (P<0.05). The diversity indices in the Jinsha River area and Three Gorges Reservoir region were significantly higher than those atother regions (P<0.05). The indices of Shannon-Wiener diversity (H’)，Margalef richness (D) and Pielou evenness (J) were employed to evaluate the ecological health of water bodies in the Yangtze River basin. The results show that the overall water quality in the main stem was amoderate pollution level. Pearson correlation analysis shows that WT (water temperature)，TN (total nitrogen)and NH3-N (ammonium)were the primaryfactors affecting the densityand biomass of phytoplankton，while DO (dissolved oxygen)was the most important factor affecting the phytoplankton diversity. Our results will provide systematic basic data for the implementation of the “10-year Yangtze fishing ban” ，and supply withscientific basis for the management and protection of aquatic ecology in the main stem of the Yangtze River.