Due to the capacity limitation, congestions caused by the excessive amount of passenger flow appear in many Mass Transit Railway(MTR) hubs. Computer simulation is one of the most effective way to solve this problem. In this paper, an identification and elimination of capacity bottlenecks method was proposed based on dynamic movement of passengers simulation. Possible optimized solution was investigated through a case study in XiErqi Station, which is the transfer hub of Line13 and Changping Line in Beijing MTR. The proposed model was validated both statically and experimentally. Two optimization measures were dicussed after digging out the passenger feature and the essence of the congestions. One is improving passenger flow organization, the other is reforming operation organization. Then the simulate experiments were done through a proprietary software developed by Beijing Jiaotong University----SRail System. The simulation result shows congestion was alleviated effectively. It is proved that the method is feasible and effective.