According to the characteristics of urban rivers, under the premise of fully considering the representativeness of river indicators, the Suzhou River was taken as the research object. Based on measured data, remote sensing images, and data collection, a river health evaluation index system composed of water resources, water environment, aquatic organisms, river habitats, and social services was constructed. The analytic hierarchy process method was used to obtain the comprehensive weights of the indicators at each criterion layer, and the indicator layer was assigned an average weight. Then the comprehensive index of river health was calculated to evaluate the health status of the river. The results showed that the comprehensive health index of the Suzhou River was 3.43, which was at a good health level. Suzhou River exhibits a spatial differentiation pattern characterized by “upstream sections outperforming downstream areas, and natural attributes surpassing social functions” in terms of overall ecosystem health. The health level of upstream sites was good and significantly better than that of downstream sites(moderate). The main factors limiting the health level of the Suzhou River were the diversity index of periphytic microfauna, the Biological Monitoring Working Party(BMWP) score system of zoobenthos, fish maintenance index, land use types, and riparian vegetation coverage. This study provides a scientific reference for the improvement of the health level and ecological function of the Suzhou River in the future.