To investigate the fish community structure and the factors influencing it in the Ulungur Lake, we collected fish samples using multi-mesh composite gill nets from 2019 to 2021. We identified 22 species in spring, summer, and autumn, belonging to four orders and six families, with seven historical indigenous species accounting for 31.8% of the total. Cyprinidae had the highest percentage of total species, with 15 species accounting for 68.2%. Throughout the year, Rutilus rutilus and Abramis brama were the dominant species in the Ulungur Lake, with Pinkas relative importance index (IRI) values of 7355.28 and 765.65, respectively. The dominant species in the Buluntuohai Lake were Rutilus rutilus and Abramis brama throughout the year, while in the Jili Lake, they were Rutilus rutilus, Perca fluviatilis, and Abramis brama. Calculation results of diversity indexes showed that the Shannon-Wiener index (H′), Margalef index (D), and Pielou index (J′) of fish communities were 0.91–1.76, 0.24–0.54, and 0.23–0.45, respectively. All of the diversity indexes H′, D, and J′ in spring were significantly lower than those in summer and autumn, and the Buluntuohai Lake had slightly higher diversity indexes than the Jili Lake. The analysis of the ABC curve showed that the abundance curve was generally above the biomass curve, and the statistical values of W ranged from –0.104 to –0.371. The disturbance degree was the highest in autumn (W=–0.226), followed by spring (W=–0.2), and the lowest in summer (W= –0.104). Additionally, the disturbance degree in Jili Lake (W=–0.307) was significantly higher than that in Buluntuohai Lake (W=–0.191). The redundancy analysis (RDA) showed that the fish community structure of Buluntuohai Lake was primarily affected by water depth, nitrate nitrogen, and water temperature, which affected the habits of fish breeding and feeding. In contrast, in Jili Lake, chlorophyll a and total nitrogen mainly affected the fish community structure, and the distribution of small omnivorous fish was positively related to the concentration of chlorophyll a and nutrients. This study found that the fish community structure in Ulungur Lake showed a trend of simplification of dominant species, miniaturization of fish, and decline of biodiversity.