Abstract: As people's awareness of environmental protection has increased, ecological protection and restoration of rivers and lakes have become hot issues, and scientific ecological health diagnosis is a prerequisite for effective governance. The Xiangxi River is a typical tributary of the Three Gorges Reservoir. Therefore, exploring its aquatic ecological health status is very important to the ecology of the Yangtze River. By collecting and organizing biotic and habitat data of the mainstream and tributaries of the Xiangxi River, a health evaluation index system for aquatic ecosystems was established. It consisted of a total of 16 indicators that are divided into three aspects: water environment, aquatic organisms, and physical habitats. Expert judgment method and entropy method were used to determine the weight of evaluation factors, and the River Health Index (RHI) was constructed to characterize the aquatic ecological status of the Xiangxi River Basin. The results showed that the overall health of the aquatic ecosystem in the Xiangxi River Basin during the impoundment period of the Three Gorges Reservoir in 2017 was good, with excellent and good samples accounting for 12.5% and 79.2%, respectively. The spatial distribution of the health level of the Xiangxi River Basin showed that the tributaries were healthier than the mainstream, and the non-backwater areas were healthier than the backwater areas. The specific performance was as follows: Nanyang River > Gufu River > Gaolan River > Xiangxi River. The water environment problems of the mainstream were relatively prominent, and the river connectivity of the tributaries was relatively poor. During the whole year, the health status of Xiangxi Bay changed, with the highest score in winter, followed by autumn, spring and summer. The research suggests that the evaluation system can be used to accurately assess the health status of the aquatic ecosystem in the Xiangxi River Basin, and it is necessary to keep focused on the water environment treatment of the bays of the Three Gorges Reservoir.