Abstract: Objectives Adding a hybrid energy storage system (HESS) to the ship power system can effectively improve the stability of the power grid. Aiming at the design of shipboard HESS planning and operation strategy under complex working conditions, a multi-objective collaborative optimization method with strong working condition adaptability is proposed. Methods Firstly, priority is given to the smoothing effect of power fluctuations in the generator set, and the hybrid energy storage's total output is determined using model predictive control (MPC). Then, the interplay between HESS capacity configuration and the energy management strategy (EMS) is taken into account, incorporating an adaptive power allocation mechanism, the harris hawk optimization (HHO) algorithm is employed to solve the optimization model, targeting the minimization of total investment cost and battery life depletion. Results The results showed that the collaborative optimization method based on MPC-HHO can effectively reduce the power fluctuation of the generator set (the average power fluctuation rate after optimization is reduced by 73.24% compared to before optimization). Meanwhile, compared with the single-layer optimization, the collaborative optimization method can effectively reduce the investment cost and battery life loss cost. Conclusions The research can provide reference for the planning and operation strategy design of shipboard hybrid energy storage systems.