Seaports consume a large amount of energy and emit greenhouse gas and pollutants. Integrated multiple renewable energy systems constitute a promising approach to reduce the carbon footprint in seaports. However, the intermittent nature of renewable resources, stochastic dynamics of the demand in seaports, and unbalanced structure of seaport energy systems require a proper design of energy storage systems. In this paper, a framework for multi-objective optimization of hybrid energy storage systems in stochastic unbalanced integrated multi-energy systems at sustainable mega seaports is proposed to minimize life-cycle costs and minimize carbon emissions. The optimization problem is formulated with reference to the energy management of the integrated multi-energy system at the seaport and considering both distributed and centralized hybrid energy storage configurations. Wavelet decomposition and double-layer particle swarm optimization are proposed to solve the multi-objective optimization problem. The real power system of the largest port worldwide, i.e., the Ningbo Zhoushan Port, was selected as a case study. The results show that, with respect to a situation with no energy storage system, the proposed approach can save 81.29 million RMB in electricity purchases and eliminate approximately 497,186 tons of carbon emissions over the entire lifecycle of the energy storage system. The findings suggest that the proposed hybrid energy storage framework holds the potential to yield substantial economic and environmental advantages within mega seaports. This framework offers a viable solution for port authorities seeking to implement hybrid energy storage systems aimed at fostering greater sustainability within port operations.