The conventional methods are difficult to achieve alignment rapidly when the strapdown inertial navigation system(SINS) under swaying base. Therefore, an anti-interference self-alignment algorithm for the swaying base is presented, which transforms the alignment problem into the Wahba problem to remove the angular interrupting, and uses the low-pass filter to filter the special force in inertial reference frame to remove the linear vibration interrupting according to the different
frequency characteristics of gravity vector in inertial reference frame and the disturbance. The simulation results show that the presented method can accomplish alignment quickly even in the presence of angular motion and linear vibration interference without the coarse alignment process.