The port integration problem in a multi-port region (MPR) is studied from the perspective of maximizing the social welfare of the external transport system in a closed region in which the ports are regarded as external transport hubs. First, the economic principle of maximizing the social welfare of the external transport system is analyzed, and a method to calculate the total internal transport cost of the external transport system is proposed. Second, the optimal scale of the port group in an MPR is determined by comparing the total internal costs for different scales of the port group. An integration method with multi-period investment and asset idling is also proposed that takes into account excess port resources in MPRs. Finally, main gateway ports in Northeast China are selected for an empirical study. Based on the findings, suggestions regarding port resource integration and cooperative operation in MPRs are presented.