In order to solve the problem of passenger flow conflict at rail transit stations connected by railway hubs, Anylogic simulation software was used to model and simulate the internal facilities and equipment and pedestrian logic of subway stations. Passenger conflict points and flow lines were analyzed according to the pedestrian density map and the passenger flow organization was optimized from two aspects of passenger flow line conflict and reasonable allocation of facilities and equipment, so as to improve the operation efficiency of the station. The results show that, due to the large passenger flow, when the railway passenger flow shares facilities and equipment with other passenger flows, it is easy to cause passenger flow conflicts, and the interweaving of different types of passenger flows will cause the confusion of flow lines and affect the entry and exit of passengers. Therefore, by channelling other passenger flow lines, setting up special facilities for railway passenger flow, rationally allocating the number of facilities and equipment, and setting staff to guide passenger flow in passenger congestion areas. After the measures are taken, the density of pedestrians in the passenger flow conflict area is reduced, and the time of passengers entering the station is reduced, which verifies the effectiveness of the measures.