Ecosystem services provided by river ecosystems rely on healthy ecosystem structure and ecological processes. The Beijing-Tianjin-Hebei urban is a typical water-deficient area. As an important part of the urban-rural integration construction, evaluating the health status of the Beiyun River Basin and discovering the weak links in the water environment is the basis for improving the health of the basin. In this study, Analytic Hierarchy Process was used to establish an evaluation index system for the Beiyun River Basin from 5 aspects including water quality, biology, habitat, hydrology, and social functions, and to assign weights to the index layer. The evaluation results showed that the health evaluation results of the Beiyun River Basin in 2019 are “sub-healthy”, and the overall health status is gradually worsening from northwest to southeast. In the middle reaches of the region, the evaluation result is "healthy", followed by the upstream, and the downstream is the worst. The results showed that areas with less human interference are in better health. The factors that affect the overall health evaluation status in the basin are the level of nutrition, biodiversity, and vegetation coverage. For the comprehensive management of the Beiyun River, the improvement of water quality and habitat ecological restoration is the key to the health of the upstream ecosystem health status. The improvement of the health status of the downstream should focus on equal emphasis on water quality and quantity, restoration of biodiversity, and improvement of the quality of the riparian ecological environment.