After the completion of the Three Gorges Reservoir, regulation of the water in the reservoir tributaries caused drastic changes in the river habitat, including a greatly reduced flow of water and formation of a 30 m deep water-level fluctuation zone. With such drastic changes, it is not clear whether the river habitat can play a positive and important role in the ecosystem health of the Three Gorges Reservoir and the maintenance of the normal functions of the reservoir ecosystem. However, existing evaluation methods cannot be easily adapted to these special habitat conditions; therefore, a new or improved evaluation method is urgently needed. Based on the analysis of a large number of domestic and international river habitat assessment index systems and the characteristics of the ecological environment of the rivers in the reservoir area, a new river habitat assessment index system, including 18 indicators that relate to river hydrology, river morphology, and the water-level fluctuation zone habitat, was constructed. The combination weighing method, which is based on the game theory and combines a subjective weighing method (the analytic hierarchy process method) and an objective weighing method (the entropy method), was used to calculate index values. We conducted river habitat quality assessments for the Dongxi River, Huangjin River, and Ruxi River, all tributaries of the Three Gorges Reservoir. The majority of the habitats scored within the range of "excellent" or "very good". This ranking corresponded with 52.6% of the sampling sites. However, 42.1% received a score within the range of "average", whereas the remaining 5.3% received a "poor" score. No site within this catchment received a score of "very poor". Our research suggests that this index system can be used to efficiently detect the status of river habitats, as it is feasible to operate and it allows easy access to scientifically sound data.