Shock is ubiquitous in life and often has a negative impact on human activities.Recently, researchers have tried various controllable materials and structures in the field of shock isolation, achieving active and semi-active control, especially various Magneto-Rheological (MR) dampers. However, there are problems such as the accuracy of the simulation model is not high and the traditional control methods and strategies cannot be used. In the current paper, a vibration isolator is proposed to improve the shock response, which is based on the MR effect. The MR damper is characterized by a differential equation model based on phase transition theory, and the dynamic model of the system is derived. Comparison of different numerical methods is presented, where the efficiency and accuracy of the different numerical methods are compared. Through the comparison, the best numerical method is finally obtained with an optimal parameter. When the system is subjected to shock, optimal control is achieved using different methods, including Chebyshev pseudo-spectral method, linear piecewise method, and Legendre wavelet method. The shock response shows the superiority of the system after adopting the control method, compared to the passive system and traditional fixed current control. This shows the effectiveness of the optimal control methods proposed in the current paper in solving shock isolation problems, especially the shock isolation problem during projectile launching.