In order to effectively reduce the vibration of the helicopter rotor transmitted from the main reducer to the fuselage, a semi-active vibration isolation system (SAVIS) with a magnetorheological (MR) damper was proposed and effective control strategies were designed. Firstly, the structural scheme and working principle of helicopter main reducer SAVIS were proposed. Secondly, the mechanical properties of the MR damper were tested, and the dynamic model of the MR damper was established based on the hyperbolic tangent model. In addition, the model errors of MR damper were analyzed and quantified. Thirdly, according to the design requirements and parameters of a helicopter, the structural parameters of SAVIS were designed. Then, the virtual prototype of helicopter main reducer SAVIS was established by using 3D drawing software and ADAMS software, and the vibration characteristics of three directions were analyzed. Finally, two controllers of equivalent skyhook and continuous skyhook were designed. The numerical analysis results indicate that compared with passive vibration isolation and equivalent skyhook controller, the continuous skyhook controller has the best vibration isolation performance and disturbance resistance, which can effectively reduce the vibration transmitted from helicopter rotor to fuselage.