The active control technology was carried out on the marine diesel two-stage vibration isolation system (MDTVIS); the active control technology was able to make up for passive vibration isolation technology in the low-frequency range. The construction of a secondary path was one of the most important sectors, which had a full impact on active vibration isolation performance. Nonlinear components comprised the secondary path, which were principally the nonlinear vibration of multi-degrees of freedom in the practical MDTVIS and the nonlinear control path in the hydraulic servo actuator. The nonlinearity was not ignorable in coping with the second path, so that the vibration isolation performance was greatly influenced by the secondary path in the active control technology with the classic adaptive comb-type filter. By combining the model reference adaptive inverse control strategy with the nonlinear robust control technology, the linearity control algorithm was designed, and then the classic adaptive comb-type filter algorithm was carried out for the new system; herein the hybrid control strategy was constructed to apply to the secondary path in the practical MDTVIS. The proposed hybrid control strategy was able to improve the initial active vibration isolation control algorithm with an adaptive comb-type filter and overcome shortcomings of the vibration strengthened in some multi-harmonic-frequency sites in the low-frequency range. The total performance of vibration isolation coupling with multi-path was improved in balance.