Based on the survey data of invertebrates and environmental factors at 28 sampling sites in Ulungur Lake from 2019 to 2021, the ecological health of Ulungur Lake was assessed by using benthic-macroinvertebrates-index of biotic integrity (B-IBI) and comprehensive biological index (CBI), and the key environmental factors affecting the two biological indexes were identified. Through the gradual screening of 34 candidate indicators, M23 (FBI index), M24 (BMWP index), M26 (relative abundance of individual gather collectors), M30 (Shannon-Wiever index) and M34 (relative abundance of individual Clingers) were finally determined to constitute the spring core indicators. M14 (the relative abundance of midges), M21 (the relative abundance of pollution-tolerant groups), M24 (BMWP index), M30 (Shannon-Wiever index) and M34 (the relative abundance of Clingers) constitute the core indicators in summer. M14 (relative abundance of midges), M24 (BMWP index), M30 (Shannon-Wiever index) and M34 (relative abundance of Clingers) constitute the core indicators in autumn. The ratio method was used to unify the index dimension, and the 25% quantile value of the B-IBI index distribution was used as the health evaluation standard. The entropy weight method determined the objective weights of seven biological indices, including Margalef, Shannon-Wiever, Pielou, Simpson, FBI, BI and BMWP. The CBI index was constructed with cumulative weights, and 95% of the quantile values of all samples were used as the health evaluation criteria. The results showed that both B-IBI and CBI indexes considered that the ecological environment of Zhonghaizi Lake was relatively healthy, the 73km Xiaohaizi Lake fluctuated from healthy to average, the Luotuobozi Lake was in sub-healthy to poor state, and the whole west of Jili Lake and Buluntuohai Lake was in average to poor level. From the time point of view, the health status of Ulungur Lake in spring and summer is better than that in autumn. Spearman correlation analysis showed that CBI, B-IBI index and 7 biological indexes were well correlated. Path analysis showed that permanganate index and nitrite nitrogen were the key environmental factors affecting the B-IBI index, while salinity and dissolved oxygen were the key environmental factors affecting the CBI index. Redundancy analysis showed that salinity and inorganic nitrogen were important environmental variables affecting CBI and B-IBI index in different seasons. The combination of the integrity index and the comprehensive biological index has a high reference value for the ecological health assessment of Ulungur Lake. In the future, measures should be taken to improve the ecological environment quality of Ulungur Lake by controlling exogenous pollution, limiting the import of nutrient-rich substances and inorganic pollutants, and reducing the salinity of the water body.