In view of the spatial and temporal imbalance of residents’ travel demands and challenges of optimal bus capacity allocation, in this paper the grand station express bus scheduling mode is introduced in the direction of heavy passenger flow during peak hours. Coordinated scheduling combining whole-journey and grand station express buses is adopted, and the station correlation calculation model is used to determine the optimal stops of the grand station express bus. Thus, a two-way bus scheduling optimization model for peak passenger flow is established with the goal of minimizing the total cost of passenger travel and enterprise operation. Finally, the nonlinear inertia weight dynamic cuckoo search algorithm is selected for the model’s solution, and the established scheduling optimization model is solved by combining basic data such as the study line’s bus Integrated Circuit (IC) card data. The effectiveness of the model is verified through a comparative study and evaluation of the solution.