This study deals with analysis and design of active vibration control algorithm for the launcher of multiple launch rocket system (MLRS). The new method proposed is that guidance and control package are equipped on launcher, not rocket, to active control motion of launcher for the first time. It has interesting advantages as follows: (1) active vibration control is more competent, more pliable, and more realizable in engineering compared to passive vibration control.(2) The guidance and control package will not be destroyed. In this study, transfer matrix method of multibody system is used to build the controlled dynamic model of MLRS. This method does not need the global dynamic equations of system and has high computational rate. Independent modal space control method and optimal control theorem are applied to design control law with feedforward and feedback control loops. The modal filters are designed as the state estimator to obtain the modal coordinates and their derivatives. Modal disturbance force observer is designed to obtain modal disturbance force. Pulse-width pulse-frequency (PWPF) modulator is used to modulate the continue control force command into discrete control force in order to avoid high non-linear control action of pulse thruster. The control force provided by pulse thruster and parameters of PWPF are obtained. The numerical results indicate that control law determined by optimal theorem integrated with PWPF modulator achieves good performance in active vibration control of launcher. This study improves the performance of MLRS in resisting impact and provides theoretical support for accurate launch.