To remove the navigation error accumulated in the boost phase of the missile’s SINS/CNS integration system, an error compensation algorithm is presented, which uses the saved IMU data and reverse attitude updating algorithm to remove the error caused by initial misalignments, and uses the off-line navigation computation to correct the boost phase error. The theory analysis show that the proposed algorithm’s performance is mainly dependent on the CNS precision , while the errors caused by gyro and accelerometer drift are tiny., the simulation results show that the proposed algorithm can reduce the velocity error to 0.012m/s and the position error to 1.12 meter, which leads to the navigation error compensated greatly.