When dealing with large passenger flows in urban rail transit, developing reasonable passenger flow control plans is a crucial aspect of operational management. When many passengers wait outside the stations, customized buses can serve as an effective way to alleviate passenger pressure. To obtain reasonable passenger flow control and customized bus connection plans, we propose an optimization method for passenger flow control and customized bus connections. Firstly, we construct a two-stage model. The first-stage model formulates the passenger flow control plan to minimize the number of waiting passengers inside and outside the station considering factors such as passenger arrivals and urban rail transit train departures and arrivals. The second-stage model develops the customized bus plan based on a time–space-state network. According to the characteristics of the model, the CPLEX solver is used to solve the first-stage model, and a Lagrange relaxation-based solution method is designed to solve the second-stage model. To verify the effectiveness of the model, a small-scale case study including two lines and five stations is designed, and the results show that the proposed method can achieve effective passenger flow control and bus connection plans. Additionally, actual data from the Chengdu Metro is used to further validate the feasibility of the method. The results indicate that the passenger flow control and bus bridging plans can effectively reduce passenger waiting time. The proposed method can effectively alleviate passenger pressure, ensure passenger travel safety, and further promote the coordinated development of public transportation.