To address the issues of high energy costs and low renewable energy utilization in port industrial parks, this paper proposes a coordinated optimization method for the operation of a port wind–solar–hydrogen–storage integrated cold–heat–electricity cogeneration system. First, a collaborative operation model of the port cold–heat–electricity system incorporating absorption refrigeration and cold storage is established to mitigate the high energy consumption and peak power demand caused by the conventional electric refrigeration mode of reefer containers. Then, a hydrogen storage–based electro-thermal coordinated control scheme is developed, in which the combined heat and power generation and waste heat recovery of electrolyzers and fuel cells are utilized to enhance the overall energy efficiency of hydrogen storage. Finally, based on the risk-averse Information Gap Decision Theory (IGDT), an uncertainty optimization algorithm for the operation strategy of the wind–solar–hydrogen–storage system is proposed to fully exploit the flexibility of the hybrid hydrogen–electricity–cold–heat energy storage system. Using operational data from Jurong Port in Singapore, a simulation model is constructed to validate the proposed approach. The results demonstrate that the proposed coordinated optimization method can effectively improve energy utilization and system economy while significantly reducing carbon emissions, providing both economic and environmental benefits for the development of green ports.