Based on the 12.5 m water depth navigation channel regulation project and the ecological features and environmental protection requirements in this river section, we explore techniques on ecological channel construction. A wide variety of ecological structures of waterway regulation was developed, and restoration engineering of artificial fish nest and ecological floating islands were also built to provide habitats for the aquatic organism. The impact of the suspended matters induced by the construction on water source sites in the tidal river was simulated and analyzed, and proper scenarios were proposed accordingly. The techniques of drive and induction of the Yangtze finless porpoise were studied based on the influence of noise, also the ecological and environmental protection measures for the overall process of construction were put forward together with the management methods. All the research results have been applied to the navigation channel regulation project in the Yangtze River below Nanjing and distinguish ecological effects have been achieved, and no environmental accidents happened.