Yan'an City, as an important area in the middle reaches of the Yellow River Basin, and it belongs to the Loess Plateau region in northern Shaanxi, China. This study took eight watersheds of Yan'an (i.e. the first tributaries are Qingjian River, Yanhe River, Yunyan River, Shiwang River and Jushui River, and the second tributaries are Beiluo River, Hulu River and Juhe River) as the objects to explore the community structure of periphytic algae and its influencing factors. Sampling analysis was conducted at 69 monitoring sections in 8 key rivers of the first and second tributaries of the Yellow River in Yan'an City in 2023 (autumn) and March 2024 (spring). This was the first time to explore the community structure composition of periphytic algae in this area and analyze the relationship between water environmental factors and community. The results showed that a total of 137 species of periphytic algae belonging to 6 phyla were identified, among which the phyla Bacariophyta, Chlorophyta, and Cyanophyta accounted for 56.2%, 20.4%, and 19.0%, respectively, the number of periphytic algae species was higher in spring than in autumn. A total of 36 species belonging to 3 phyla were identified as dominant species, mainly diatoms. The average density of periphytic algae in autumn and spring was 3.88×105 ind/cm2 and 2.57×105 ind/cm2, respectively, and the density in autumn was significantly higher than that in spring. The key species maintaining the stability of the community in autumn were Nitzschia acicularis, Dactylococcopsis acicularis, and nothrix planctonica, while in spring, it was Pseudanabaena limnetica. The interaction between the periphytic algae communities in spring was stronger than that in autumn, and the stability and resilience of the communities were also stronger in spring. The flow rate was not only the main environmental factor influencing the structure of the periphytic algae community in autumn and spring, but also a common environmental factor that affects the structure of periphytic the algae community in autumn and spring. In addition, ammonia nitrogen, dissolved oxygen, and total phosphorus were the main environmental factors affecting the structure of the living algae community in autumn, and water temperature and pH value were the main environmental factors affecting the structure of the algae community in spring. The research results provided scientific data support for the formulation of water ecological management systems in the basin, the stability of water ecosystems and the maintenance of aquatic biodiversity. It was of great scientific significance for understanding water ecological functions and promote the construction of ecological civilization and high-quality development of the Yellow River Basin.