Aiming at the measurement information error caused by time delay, put forward the estimation and compensation method for information transmission delay. At first, analyze the influence of reference information on transfer alignment, and establish model according to reference inertial navigation time delay. Then, derivate transfer alignment observation equation of time delay condition. At last, carry out simulation test. The results of the simulation show that the delay time can be accurately estimated. The method can effectively suppress the divergence of the filter caused by master inertial navigation information measurement time delay, and improve the accuracy of the transfer alignment.