The Xinliuhe shoal protection project and Nanshatou channel submerged dike are very important parts of Yangtze estuary deepwater channel regulation project. With the adverse effect of river regime’s changes, the river bed outside the flexible mattress edge of the locally regulating structure keeps scouring deeper and deeper, which affects the safety of the structure. This protection is implemented to ensure the regulation effect. Based on the experience of Yangtze estuary deepwater channel regulation project, through water current analysis and typical constructions, we carried out a series of optimization and improvement in ship equipment, flexible mattress machining and construction technique, and filled sand bags and laid flexible mattress successfully over 30 m under the water for the first time in the Yangtze estuary, which met the design requirements.