In order to improve the problem of the unreasonable structure of inland water transport development, considering the game relationship between cargo owners, shipping enterprises and waterway network planners, a bi-level programming model for the optimization of waterway network is constructed in this paper. The upper-level model takes the minimum sum of the construction cost and the operating cost of the waterway network optimization plan as the objective function, and the lower-level model adopts the waterway network assignment model based on the user equilibrium. Finally, by taking Shandong Province as an example, the genetic algorithm is used to solve the model, and three evaluation indicators are selected to compare and evaluate the results of the optimized plan and the original plan. The results show that the Shandong Province waterway network optimization scheme obtained in this bi-level programming model is more superior to the original program, which improves the actual transportation efficiency of the waterway and verifies the effectiveness of the proposed model.