To improve the vibration isolation performance of the one-stage isolation system for marine equipment, the influence of the semi-active magnetorheological (MR)damper and base mass on the vibration transmission of the system is studied. An improved Bingham model verified by experiment is adopted to describe the nonlinear damping force of the MR damper, and the dynamic model of the two degree of freedom unconstrained isolation system considering the influence of the base mass is established. The analytic solution for primary resonance of the isolation system is obtained based on the averaging method which is verified by numerical method. The influence of the main system parameters on primary resonance of the isolation system is studied by taking the force transmissibility as evaluation index. The results show that the increase of base mass can reduce the natural frequency and the isolation effect at the vibration isolation zone. The performance of the isolation system can be improved by increasing the control force and zero force velocity of MR damper. The damping increase of MR damper can improve the isolation effect in the resonance region, but have opposite effect on the vibration isolation region.