(1) Background: River health assessment provides the foundation for sustainable river development and management. However, existing assessments have no uniform standards and methods. (2) Methods: The combination weighting method was proposed, drawing on the advantages of subjective and objective weighting methods. To comprehensively investigate the river health level, an index system based on 16 indices selected from river morphology, river water environment, riparian condition, and social services level was established. The method and framework were applied to the Beijing section of Yongding River in China. (3) Results: The comprehensive weights of river morphology, river water environment, riparian condition, and social services are 0.1614, 0.3170, 0.4459, and 0.0757, respectively. The river health comprehensive index of Yongding River is 3.805; the percentages of excellent, healthy, sub-healthy, unhealthy, and sick river segments are 0%, 11%, 69%, 20%, and 0%, respectively. (4) Conclusions: The results indicate that Yongding River is in a sub-healthy state, and the riparian condition is the key factor that affects the river ecosystem health. Health level exhibited a remarkable spatial variation, mainly influenced by anthropogenic activities, and effective measures are needed to minimize the impact in fragile ecological areas.