Science and technology innovation practice in the implementation of the Yangtze River estuary deepwater channel construction project and the Nanjing Yangtze River deepwater channel construction project is worthy of reference. Its significance lies in science and technology innovation management, strengthen the major waterway construction during the implementation period, should pay attention to strengthening the consciousness of innovation management of science and technology, make full use of the supporting platform of innovation of science and technology, handling technology support and innovation of science and technology, basic research and technology innovation, the construction units and construction units to guide the play its positive relationship etc., continuous innovation and technology innovation management.