The AC/DC hybrid ship power system has the problems of small line impedance and similar fault currents in adjacent sections. Hence, the protection method based on the principle of time and current is difficult to ensure the protection selectivity. This paper proposes a hierarchical collaborative protection method based on the principle of layer-by-layer verification, which uses the evaluation system of system electrical kinds, fault hazard, protection particularity, insurance priority and special load requirements to determine the protection stratification and the protection configuration of each layer. Based on the layer-by-layer verification and modification, the selectivity of the global protection of the integrated power system is realized. Finally, the feasibility of the proposed hierarchical collaborative protection method is verified by SIMULINK simulation.