Abstract: The problems, such as time alignment, multi-rate filter, unequal interval and measurement delay, were involved when information was fused in inertial navigation system /scene matching navigation system(INS/SMNS)integrated navigation system. In order to solve them, a solution, based on the fact that INS/SMNS integrated navigation system was applied in terminal guidance generally and the relation between Kalman filter and measurement, was presented. Extrapolation was applied to the align time, the system was discretized in unequal interval and the multi-rate filter was designed, the measure delay was eliminated by software. Analyzing the filtering accuracy of the common Kalman filter, the Kalman filter without measurement delay and the presented solution, the results demonstrate that the method presented here has high accuracy.