With the economic globalization continuing to advance, coastal port cities have enjoyed increasingly prominent status and roles as the link between the sea and the land and an important window of foreign trade and exchanges. However, port cities, while embracing rapid development, have also produced a significant impact on natural resources and the ecological environment. Ecological environment protection has become a must-consider factor for sustainable development of port cities. To secure coordinated and sustainable development of ports and cities, this paper utilizes the system dynamics theory and approaches the subject from driver analysis. In the traditional port-city collaboration system model, indicators of ecological perspectives such as land resources and environmental protection are introduced to build a dynamic model for the spatial evolution system of port-city coupling system based on ecological protection, and the dynamic mechanism of port-city spatial relation evolution is analyzed in depth with a case study of Dongdu Port Area of Xiamen Port. The model’s simulation results show that from an ecological perspective, the spatial distance between the port and the city is critical to their sustainable and coordinated development. Only after the port-city spatial distance increases moderately can the development efficiency of the port-city system welcomes a relatively significant increase. Managing the port-city distance well has a significant driving effect on capacity enhancement of the port and economic development of the city. This provides a theoretical reference for further studies on port-city coordinated and sustainable development and provides constructive suggestions for the government to make relevant decisions.