The propulsion systems of hybrid electric ship output and load demand have substantial volatility and uncertainty, so a hierarchical collaborative control energy management scheme of the ship propulsion system is proposed in this paper. In a layer of control scheme, the traditional perturbation algorithm is improved. Increasing the oscillation detection mechanism and establishing the dynamic disturbance step length realizes the real-time stability of maximum power point tracking control. In the second-layer control scheme, the power sensitivity factor and voltage and current double closed-loop controller is introduced. By designing a two-layer coordinated control strategy based on the dynamic droop coefficient, the problem of voltage and frequency deviation caused by load switching is solved. In the third-layer control scheme, due to the need of the optimal scheduling function, the multi-objective particle swarm optimization algorithm was improved through three aspects: introducing the mutation factor, improving the speed formula, and re-initializing the strategy. Compared with other algorithms, this algorithm proves its validity in day-ahead optimal scheduling strategy. The superiority of the hierarchical collaborative optimization control schemes proposed was verified, in which power loss was reduced by 39.3%, the overall tracking time was prolonged by 15.4%, and the environmental cost of the diesel generator was reduced by 8.4%. The control strategy solves the problems of the steady-state oscillation stage and deviation from the tracking direction, which can effectively suppress voltage and frequency fluctuations.