Periphytic algae usually attached stably on the substrate, and its community structure is mainly affected by environmental factors. Meanwhile, periphytic algae are important biological indicators of aquatic environment. In this study, we examined the community structure of periphytic algae in the high water level phase in 5 different areas of Lake Poyang (the main channel area, West wetland, Nanji wetland, Cuoji Lake, and Southeast Lake), including biomass, dominant species, and biodiversity. The relationship between environment and periphytic algae was analyzed. This study can provide basic data for aquatic environment protection and water resources use of Lake Poyang. The results show that Bacillariophyta, Chlorophyta, and cyanobacteria are dominant in the periphytic algae community of Lake Poyang. There are obvious spatial differences of periphytic algae biomass in Lake Poyang. The biomass of periphytic algae in the main channel is highest, averagely 419 mg/m²; followed by Southeast Lake, averagely 322 mg/m². The average biomass of periphytic algae in the Nanji wetland and West wetland are 172 and 52 mg/m², respectively. The biomass of periphytic algae in the main channel is lowest, averagely 9 mg/m². The dominant populations of periphytic algae in the main channel are Bacillariophyta and Chlorophyta, while the dominant populations in the other four regions, i.e. West wetland, Nanji wetland, Cuoji Lake, and Southeast Lake, are Bacillariophyta. The redundancy analysis showed that the distribution of periphytic algae community in the high water level phase in Lake Poyang is closely related to physical and chemical factors such as total phosphorus, electrical conductivity, pH value, total nitrogen, nitrate nitrogen, and suspended solids. The main channel of Lake Poyang is connected to the Yangtze River with high water flow velocity. West wetland, Nanji wetland, Cuoji Lake, and Southeast Lake are seasonally connected with Lake Poyang. They are connected to the main body of Lake Poyang in the high water level phase and are separate regions in the low water level phase. The different regional characteristics of five regions are one of the important reasons for the spatial variations of periphytic algae community structure. The diversity index of periphytic algae indicated that the water body of Lake Poyang is in a moderately polluted state.