To ensure navigation safety during the pre-advance construction period of the second-stage cofferdam at the main branch project in the lower reaches of the Ganjiang River, a two-dimensional hydrodynamic numerical simulation method was employed to model and analyze the hydrodynamic processes of the temporary navigation channel under various construction scenarios and working conditions. Threshold navigation flow conditions and corresponding improvement measures were proposed. The results demonstrate that retaining the upstream section of the first-stage cofferdam serves a flow-diversion function, thereby improving local navigation flow conditions. Although the pre-advance construction alters the local flow direction in the river channel and affects lateral flow velocities in certain sections of the temporary channel, its overall impact on navigation flow conditions remains limited. However, retaining the downstream cofferdam of the first stage increases the diversion ratio of the left temporary channel, significantly expanding the range where longitudinal flow velocities exceed 2 m/s, which adversely affects navigation. After implementing adjustments, the numbers of cross-sections in the temporary channel with lateral flow velocities exceeding 0.5 m/s under current conditions, after removal of the existing cofferdam, and during the pre-advance construction of the second-stage cofferdam decreased by 66.7%, 70%, and 66.7%, respectively, compared to pre-adjustment conditions, indicating a notable improvement in navigation conditions.