To alleviate urban traffic pressure and reduce congestion costs, this paper constructs a multi-objective mixed integer programming model for optimizing the timetable and allocation of passenger and freight wagons in the case of operating cross-line trains. The model aims to minimize passenger waiting time and train operation costs, thereby optimizing the timetable and distribution of passenger and freight wagons to enhance the transport capacity. The paper conducts data experiments using the Beijing Subway Line Fangshan and Line 9 as a case study, and utilizes the optimization solver Gurobi for solution. Experimental results demonstrate that the timetable determined by the model can better meet the requirements and constraints. Compared with the scenario of not operating cross-line trains, operating cross-line trains on subway lines can significantly reduce average passenger waiting time, fully utilize redundant transport capacity, and reduce train operation costs.