the Yangtze River Delta (YRD) has established a large-scale container port system with seaports and Yangtze ports as the mainstay and including other riverports and dry ports, occupying a prominent position in the pattern of national and even the global shipping development. Considering the new trend that the theoretical paradigm of port research has shifted from “spatial” to “network”, and that the focus of research goes from seaports to both seaports and inland ports, this study brings the complexity and uniqueness of the development of the port system in the YRD into the picture. By analyzing the influence of globalization, specialization, marketization, transportation, and greenization on port system development and its pattern formation, this paper elaborates on the gradient process of transportation and services allocation from the coast to the riverside and then to the inland. The evolution of port system is considered to have a temporal gradient between spatial-level transportation expansion and network-level services upgrading, and it is also believed that there is a spatial gradient in logistics supply chain terminalization between coastal and inland areas. Combined with the quantitative analysis from 200 5 to 2020, after entering the stage of port regionalization in the YRD, the container volume is distributed from coastal concentration to inland decentralization at the spatial level, while at the network level, port and shipping service enterprises (PSSEs) maintain a relatively centralized distribution along the coastal areas. At the same time, container volume growth rate fluctuates down, number of PSSEs growth rate fluctuates up, which trend is notable in the seaport. Currently, port regionalization in the YRD is still incomplete; the degree of logistics supply chain terminalization of ports in inland areas is relatively low; and the synergy between spatial and network in the entire YRD region has not yet been formed. This study tries to answer the question of the relationship between different types of ports in the complex port system, which can enrich the theoretical and empirical results of port system research and guide the practice of port and shipping in the YRD.