Under the new development pattern of “dual circulation” in China, it is of great theoretical and practical significance to study the spatial pattern and evolution law of port systems. This study takes the port system in the Yangtze River Delta Region (YRDR) as an example, based on the panel data from 2000 to 2019, analyses the spatial pattern and evolution characteristics of port domestic trade throughput (PDTT) and port foreign trade throughput (PFTT) from the perspective of dual circulation. The key influencing factors in the evolutionary process are explained, and the spatio-temporal evolution characteristics of the two types of port throughput are compared. The results show that (1) in spatial evolution, the PDTT and PFTT of the port system in the YRDR fluctuate and increase significantly, showing a typical three-level echelon structure in space. (2) From the perspective of spatial equilibrium, the two types of port throughput are markedly discrete; however, the degree of agglomeration of PFTT is greater than that of PDTT. (3) In spatial patterns, the centers of gravity of PDTT and PFTT are distributed in Suzhou and Jiaxing, respectively. Both are distributed from northwest to southeast. However, the rotation angle of PFTT was larger, and the north-south differentiation was more evident than that of PDTT. (4) In influencing factors, the throughput pattern of the port system in the YRDR is driven by multiple factors, and some differences exist in the driving mechanism between PDTT and PFTT.