Aiming at solving the problem of navigation congestion caused by insufficient navigation service capacity of locks, the linkage mechanism of `congestion charge-overturning subsidy' is studied. The prospect theory is used to analyze the navigation behavior of shipowners, and an optimization model based on congestion charge-overturning subsidy is established to reveal the freight sharing law of the two dam-crossing modes under different congestion charge and overturn subsidy levels. According to the number of ships arriving, the warning level of navigation congestion is then divided. The selection probability of dam-crossing mode, the change trend of total cost of dam-crossing and the benefit of navigation carbon emission reduction are explored. Finally, taking the Three Gorges Project as an example, the validity of the above model is verified. The results show that under different warning levels, with the increase of congestion charges, the probability of dam-crossing selection of the five-level lock decreases continuously. Furthermore, the implementation of a reasonable congestion charging-dumping subsidy policy can reduce the total cost of crossing the dam and carbon emissions by up to 62.7% and 49.5%, respectively. While achieving a balanced freight sharing, it produces both good economic and ecological benefits.