The river reach of Tongzhou shoal and Baimao shoal is influenced by both river discharge and tide. The hydrodynamics is complicated and river bed is active in siltation and erosion. Tongzhou shoal and Baimao shoal are two major obstacle shoals of the 12.5 m deepwater channel extending up to Nanjing in the Yangtze River. Based on hydrodynamic research results of the engineering river reaches, numerical and physical models are used to study the overall plain plan, tooth groin elevation of submerged dike for Tongzhou shoal and Baimao shoal, middle channel transition section elevation of Tongzhou shoal, and the suggested optimization plan. It is concluded that the optimization suggested plan can control the erosion and backward trend of Tongzhou shoal and Langshan shoal, stabilize the discharge diversion of the two branches, and form the bifurcation layout of north and south channels.