Regarding the construction of the ecological channel of North Channel and South Passage planned in the Yangtze River Estuary，this paper analyzes the regional environmental characteristics and channel development needs，combs and summarizes the ecological construction of the deep-water channel in the Yangtze River Estuary，puts forward the core and construction mode of the ecological channel construction in the Yangtze River Estuary. The conclusions are as follows：1）The construction of the ecological channel of South Passage and North Channel should be based on ensuring the stability of the river regime. 2）It needs to form a linkage layout with tidal flat protection and ecological function area protection. 3）It is necessary to actively develop and apply the ecological structure，build the “artificial ecological reefs” and optimize the comprehensive environment. 4）Itis necessary to realize the resource and ecological utilization of channel dredged soil in combination with the demand of tidal flat sediment resources and the demand of channel construction for embankment sand. 5）It is necessary to strengthen the scientific management and ecological compensation system in the construction and operation，etc.