In order to solve the congestion problem of daily rail transit station and improve the passenger transportation efficiency of subway stations, AnyLogic simulation software was used to simulate the subway station, the pedestrian density map of subway stations was obtained, the bottlenecks of subway stations was analyzed, and measures from the perspectives of pedestrian streamlines and the layout of facilities and equipment in the station was proposed. The results show that the security inspection and the platform-level escalator group of the subway station are usually the congestion bottleneck area of the subway station. Improving the congestion in the security inspection area and the exit area of the escalator is the key to improve the passenger transportation efficiency of the subway station. It is an economical and efficient measure to add an independent security inspection system at the security checkpoint and arrange staff to guide the flow of people in congested areas in due course. After the measures taken, the pedestrian density in the congestion are decreased, which verified the effectiveness of the optimization measures. This method can provide a reference for the daily passenger flow organization and management of subway stations.