Aiming at the problems of the sensitivity to the shock circumstances and poor dynamic accuracy under shock loads of the strap down inertial system, the impact capacity of MEMS gyroscope, quartz accelerometer and the framework has been analyzed in this paper. The structure design method of the strap down inertial system under the shock loads has been proposed. First of all, the sensor orthogonal distribution has been guaranteed by the structural design. Second, a simple and practical way to isolate the impact of the structure has been designed. The finite element simulation and the physical test show that this method is reliable and effective.