Air-to-Air Missile (AAM) should have the capability of being launched at any time, so how to hold the accuracy of initial alignment for a long time after entering the fight airspace is a critical problem. For the sake of transfer alignment application in the real AAM, a method for long-time rectification in flight with time delay compensation was studied. A Kalman filter for long time transfer alignment was designed on the basis of the general transfer alignment model. Simulations were made based on the real IMU and the 6 DOF mobile platform, and analysis was made to the simulation results. The result shows that the algorithm can effectively compensate for the time delay error, and realize the transfer alignment with a high accuracy (less than 0. 2°) in long-time rectification.