Abstract: In order to explore the development of Chongqing port cluster transportation system and promote the positive cycle of Chongqing port cluster development, the system dynamics model of Chongqing port cluster transportation system is constructed through various factors among Chongqing port clusters. According to the causality diagram and dynamic flow diagram of the model, the qualitative and quantitative relationships between the sub-structures of the model and the system elements are obtained through the regression analysis of parameters and the construction of state equation. The Vensim software is used to simulate, and the validity and consistency of the model are analyzed and verified by comparing with the actual collection and distribution system. Finally, through the simulation of various collection and distribution modes of Chongqing port group, it is concluded that Chongqing port needs to strengthen the development of railway and waterway collection and distribution, which points out the direction for the future development of Chongqing port.