As a key link in the maritime supply chain, reasonable investment in ports can enhance the location advantages of the hinterland. In this paper, the investment problem of multi-port areas considering disasters under uncertain demand is studied, an optimisation model is established with the objective of minimizing the total system cost and maximising the efficiency of port operations, and an analysis of the port cluster in the Yangtze River Delta region is carried out to obtain an investment plan for the port cluster with reasonable results. This investment optimization can provide some reference for government investment in the construction of ports.