With the rapid development of social economy, strong human activities including the Three Gorges Project have had a great impact on the natural evolution of the lower Yangtze River, and further affected the river’s natural and social functions. In this research we establish an evaluation system containing fourteen indicators to represent the impact of river channel evolution on five major functions of river channel, namely, flood control, navigation, bank and shoal protection and utilization, water resources, and water ecological environment. In subsequence, we determine the weights of the indicators by integrating expert scoring method and AHP method, and formulated the quantification and scoring standards of each indicator. Application to the Shiye sandbar branch in the lower Yangtze River manifests that, after the impounding of the Three Gorges Project (2019), most indicators have improved to varying degrees compared with those before the impounding (2002). Yet, problems still exist. Such problems include the stability of river bank, the impact of water-involved project groups, and the reduction of aquatic biodiversity. The evaluation index system and conclusions of this paper is of popularization significance for the protection and governance of the Yangtze River.