Port-city system is a complex and integral system, and it can be simulated by system dynamic method, which is used to be employed to solve nonlinear problems. Based on the causality of the every element in the port-city system, the authors analyzed the feedback relation and logical relation among the system variables and system structure. A system-dynamic flow chart and correlation equations were put forward with VENSIM software, the quantitative relation was described, and the model was debugged. The development trend of the main influence factors in port-city system was simulated. By changing the parameters values of variables in the model, we studied the influence degree of each related factor. It is found that: 1) Foreign trade throughput of port play an important role in the development of export-oriented economy. 2) The development of primary industry and secondary industry affects most of the water transportation demand. With the constant increase of tertiary industry proportion in the industrial structure, the demand of national economy for water transportation decreases gradually. 3) Water transportation presents a kind of oversupply development situation, so port construction should properly slow down. 4) With the development of ports, its direct and indirect contribution to urban economy has been continuously increasing, but contribution rate will be continuously decreasing. Port-city system is a complex and integral system, and it can be simulated by system dynamic method, which is used to be employed to solve nonlinear problems. Based on the causality of the every element in the port-city system, the the feedback relation and logical relation among the system variables and system structure. A system-dynamic flow chart and correlation equations were put forward with VENSIM software, the quantitative relation was described, and the model was debugged. The development trend of the main influence factors By changing the parameters value of variables in the model, we studied the influence degree of each related factor. It is found that: 1) Foreign trade throughput of port play an important role in the development of export -oriented economy. 2) The development of primary industry and secondary industry affects most of the water transportation demand. With the constant increase of tertiary industry proportion in the industrial structure, the demand of national economy for water transportation tends gradually. 3) Water transportation presents a kind of oversupply development situation, so port construction should properly slow down. 4) With the development of ports, its direct and indirect contribution to urban economy has been continuously increasing, but contribution rate will be continuously decreased.