In allusion to harmonic interference and harm in application of marine AC electric propulsion system, the advantages and disadvantages of several marine harmonic suppression methods applied at present, including PF, APF, multi-pulse rectifier filter and PWM rectifier, are compared, and a hybrid filter combining PF with APF is designed from the perspective of practical application and applied to marine electric propulsion system; the system structure and control circuit working principle are introduced. Contrastive analysis of PF and hybrid filter system is conducted based on practical ship test data, from which it is concluded that the hybrid filter system has better filtering effect and higher cost performance, thus a new solution is provided for harmonic suppression design of marine electric propulsion system of fishery and other industries.