In order to measurement noise of missile overload, an adaptive filtering algorithm on missile borne MEMS accelerometer is proposed. This method set condition threshold according to overload variation, carry out adaptive adjust filtering coefficient, improve missile overload accuracy. Simulation results show that the adaptive filter can effectively suppress the error of standard deviation of noise signal from 0.020 6 m/s2 before to 0.006 1 m/s2, and achieve a good balance between smoothness in low overload and sensitivity in high overload.