Abstract: The Chaobai River is an important water source of Beijing. It is essential to understand fish diversity and river health for the conservation of the aquatic ecosystem. Fish samples in the Huairou section of the Chaobai River were collected in September 2022 and April 2023. A fish-index of biotic integrity (F-IBI) was established to assess river health. The results showed that: (1) According to historical data and field surveys, 54 native fish species were identified, belonging to 43 genera, 25 families and 7 orders. Fish species from Cyprinidae were dominant, accounting for 66.67% of the total number of the native species. (2) Fish diversity analysis showed that the Shannon-Wiener, Margalef, and Pielou indices were highest in the Yanqi River, while the Sha River had the lowest values. (3) Seven out of 26 candidate indicators were screened to develop the core F-IBI indicator system, including the Shannon-Wiener diversity index, percentage of Perciformes species, percentage of Cobitidaes individuals, percentage of Cyprinidae individuals, percentage of individuals inhabiting the middle and lower water layers, percentage of individuals that spawn viscid eggs, and the total of individuals. (4) The evaluation results of F-IBI indicated that the health status of the rivers was generally fair to above-fair, with no points classified as very poor. The results from the traditional step method and ration method can be mutually referenced. This study revealed that Pseudorasbora parva and Rhynchocypris lagowskii were the two dominant species in the Huairou section of the Chaobai River. The F-IBI indicator system comprehensively reflected the community structure and effectively evaluated the health status of the Huairou section of the Chaobai River.