Abstract: The South Channel of the Yangtze Estuary is one of the key areas which play a navigation and ecological role for the Yangtze Estuary and even the Yangtze River. In order to evaluate the influence of the first-stage regulation engineering at the South Channel of the Yangtze Estuary on the adjacent sea area and the ecological sensitive area of Jiuduansha wetland, according to the navigation, ecology, resource conservation and coordinated development functions of the waterway, a comprehensive and independent evaluation index system for regulation engineering at South Channel of Yangtze River Estuary was set up. The analytic hierarchy process of group decision was used to give weights, the fuzzy synthetic evaluation method was used to evaluate the health level of the channel, and the sensitivity analysis was conduct on the results. The results show that the membership degree of excellent of ecological health level for the South Channel Waterway engineering is the highest, demonstrating that the ecological effect of the waterway engineering is good. It is proved that the waterway regulation engineering has not destroyed the functions of the waterway and ecologically sensitive areas, and greatly improved the navigation function of the waterway, but had little effect on improving the biological habitat of the waterway and Jiuduansha wetland. The sensitivity analysis results show that the evaluation results are not sensitive to criterion weights of 20%~90% fluctuation, having high stability and reliability.