Recently with the boom of economy and foreign trade, the multi-modal transport system, e.g. sea-railway transportation, rail-road transportation, etc. is emphasized by many countries to facilitate the foreign trade. Therefore, the infrastructure for the multi-modal transport system is becoming more important. This paper tries to analyze the elements which influence the efficiency of the railway system in the container port. Firstly, this paper introduces the function and operational procedures of the rail system in the container port. Secondly, this paper sets up the theoretical model of loading-unloading line subsystem in the container port based on the Generalized Stochastic Petri Nets. Thirdly, this paper simulates the Petri Nets of handling subsystem of the railway system based on Stpnplay Software. Finally, this paper utilizes the Markov chain as the same configuration as GSPN to achieve the steady probability in order to discuss the performance indicators of efficiency and throughput of the loading-unloading lines of the railway system in the container port.