A 6-DOF vibration isolation system with magneto-rheological damper (MRD) based on Stewart mechanism was designed to reduce the mechanical vibration more effectively. To make the isolation system perform well, an effective control method was also proposed. Using the linear multibody systems transfer matrix method (MSTMM), the dynamic model of the MRD 6-DOF vibration isolation system was established to obtain the dynamic characteristics. Firstly, based on the test mechanical property of magnetorheological damper, the electromagnetic coupling model of magnetorheological damper was established. Secondly, the transfer equation of 6-DOF vibration isolation system was established by linear MSTMM. And the state space equation was derived using the modal superposition method, which was based on the augmented eigenvector and body dynamics equation. Thirdly, the linear quadratic Gaussian control method of MRD 6-DOF vibration isolation system was designed. Finally, the numerical simulation was carried out. The results showed that MRD 6-DOF vibration isolation system with optimal control improved the dynamic performance of mechanical equipment effectively. Compared with passive vibration isolation system, the translation of the vibration isolation system in the X, Y, and Z directions, as well as the rotation around the X axis, Y axis and Z axis were reduced by 51.85%, 58.71%, 64.43%, 75.43%, 66.45% and 52.87%, respectively. Similarly, the percentage drops were 50.00%, 56.16%, 34.94%, 53.09%, 38.14% and 46.76% compared to the PID control based vibration isolation system, respectively. The established dynamic model and control strategy provided theoretical basis for relevant vibration isolation tests.