The development of shipping increases the number of ship lock extension projects in inland navigation hydro-junctions. The extension of ship locks on the basis of existing structures will inevitably change the boundary conditions and hydrodynamic characteristics of the river reach near the existing project, which in turn will impact the operation of the existing structures. Based on the ship lock extension project in Fuchun River, the impact of ship lock extension project on the existing structures and its improvement measures were analyzed through the overall physical model test. Since the ship lock in Fuchun River is located in the branching channel of gorge area, the diversion ratio of branching channels has changed obviously due to the construction of ship lock extension and the guide wall. The water level and flow of the left branch, which is the main channel, increased and affected the power generation and flood discharge adversely. In order to reduce the adverse influence, it is suggested to excavate a flood channel between the partition wall of the right branch and the mid-channel bar to maintain the original diversion ratio of the river to the fullest extent. However, the flood channel is close to the downstream entrance area, and the navigable flow conditions in this area do not meet the requirements under the influence of concentrated flow in the flood channel. Therefore, navigation condition of the ship lock and the function of power generation and flood discharge are incompatible. Finally, the innovative measure of controlling diversion by setting control gate at the entrance of branching channel is put forward. By regulating the diversion ratio of the two branches, the problem of the interaction between ship lock navigation and hydro-junction operation can be solved.