In view of the problem of initial alignment of the moving base caused by the disturbance when an individual shooter carries the small ammunition on the shoulder, an initial alignment method that can reduce the disturbance caused by the irregular movement of the human body is studied.In view of the characteristics of the moving base alignment of the inertial guidance system, an error model is established.The accelerometer is used to acquire the data in real time for coarse alignment.In the process of refined initial alignment, the extended Kalman filter is used and the errors of position and velocity are taken as an observation for estimation.The attitude matrix is updated in real time, and finally the accuracy of the proposed method is analyzed by using the covariance of each axial attitude angle.The results show that using this method can effectively improve the initial alignment accuracy of the small ammunition carried by an individual shooter.