The error of inertial measurement device leads to computation bias of flight parameters, so as to affect the accuracy of the missile directly. So separation of the tool error coefficient using experimental data and sending it back to the math platform is a primary way to improve the missile's hit accuracy. The SINS instrumentation error separation model was built based on quaternion and then the model was used for separating the coefficient of instrument error. The simulation and experimental result verify the validity of the instrument error model. The coefficient separation results are better than the traditional Euler angle error model. The SINS model's establishment provides an important reference for engineering practice.