In view of the variety of aquatic organisms in the 12.5 m deepwater channel in the Yangtze River below Nanjing,how to effectively control and alleviate the adverse effects on the environment during the construction of the channel project is a new subject in front of the builders of the deepwater channel.For this,in the second phase project of the 12.5 m deepwater channel in the Yangtze River below Nanjing,we research and development the new ecological structures of the renovation of the building,strengthen the site monitoring,implement the supervision system,set up the downtime and eco-compensation,which have gained useful practice and exploration,as well as achieved remarkable results in the environmental protection construction.It can provide reference for other projects.