Urban rail transit passenger flow corridor areas connect the urban core area with the main functional areas of different urban circles, and are regions where urban spatial resources and economic activities are concentrated. Their transportation efficiency has a significant impact on the capacity of the rail transit network and socio-economic activities. In view of this, for the urban rail transit passenger flow corridor areas, based on the "one main line with multiple branches" topological structure of passenger flow corridors, a multi-objective nonlinear optimization model is proposed with the objectives of enterprise operation cost, passenger travel cost, and load factor imbalance coefficient. The model takes the departure frequency and marshalling scheme as decision variables, and designs a NSGA-II algorithm for solving. Taking the passenger flow corridor from Huilongguan/Tiantongyuan to Zhongguancun in Beijing as an example, the effectiveness of the model is verified. The results show that the model can effectively match the multi-directional travel demands between job-housing clusters. To verify the optimization effect of the model, an improved distance-based optimal solution solving method is proposed. The obtained optimal solution shows that the passenger travel time, enterprise operation cost, and load factor imbalance coefficient are 2639.170, 103716.24, and 0.086 respectively. Compared with the independent operation scheme of this line, the passenger travel time is reduced by 14.09%, the load factor imbalance coefficient is reduced by 43.01%, and the enterprise operation cost is increased by 17.22%. At the same time, in complex line networks, the restrictions of the maximum carrying capacity of the main line section and the minimum service level of the branch section have a great impact on the effect of the optimization scheme. By increasing the upper limit of the main line capacity, the study investigates the impact of capacity restrictions on the optimization of train operation schemes in passenger flow corridors. The results show that under the condition of improving the line carrying capacity, the diversity of Pareto solutions increases, passenger travel time is significantly reduced, and the balance of service is improved. The research results provide corresponding experience and guidance for further optimizing the cross-line operation scheme and actual operation.