The novel mixed passengers and freights transportation mode has brought both opportunities and challenges to the operation and management of high-speed railway in China. This paper proposes an integer linear programming model for the collaborative optimization problem of train schedules and freight allocation on a shared freight and passenger high-speed railway system to minimize the train dwell time, the number of detained freight, and operating costs, where the arrival and departure times of trains, the formation of trains, and the freight allocation are the decision variables. Then, extensive numerical experiments based on the operational data of the Beijing-Shanghai high-speed railway line are conducted to verify the effectiveness of the model, and the CPLEX optimization solver is used to solve the problem. The results show that the method proposed in this paper can improve the train capacity by flexibly deciding the train schedule and increasing the train composition while minimizing the impact on the quality of passenger service. Compared to the optimization method with fixed train timetables, the integrated optimization method can significantly improve the freight transportation capacity while only a slight increase in stopping time, providing theoretical support for the relevant operational departments to make mixed transportation plans.