Abstract: River habitat is an important component of river ecosystems which play an important role in maintaining river health. River habitats assessment can provide an important basis for the protection and restoration of degraded river ecosystems. We established an evaluation system which is specific to the characteristics of the mainstream in the Yangtze River, with ten indexes from three aspects of the river physical morphology, riparian zone habitat and water environmental characteristics. Based on the evaluation system, comprehensive assessment of river habitats was carried out from August to September 2017 in 127 survey sections of three regions, which are the lower reaches of the Jinsha river, the Three Gorges Reservoir, and the middle and the lower reaches of the Yangtze river. The evaluation results show that the river habitat comprehensive index (RHI) of the three regions are 133.9, 124.6 and 130.8, respectively, which were all at the “good” level. The river hydrology and disturbance by human activities are the main driving factors affecting the habitat quality of the lower reaches of the Jinsha River. The river canalization and hardening degree, riparian vegetation cover and riparian vegetation bandwidth are the main driving factors affecting the habitat quality of the Three Gorges Reservoir and the middle and lower reaches of the Yangtze River. In the next step, we should continue to protect the integrity of aquatic habitats in the upper reaches, to carry out restoration of the riparian, the bottomland and the connectivity of rivers and lakes in the middle and lower reaches, as to build an ecological corridor and biodiversity conservation network of the Yangtze River.