The pointing accuracy of phased array antenna is very important to the radar system.There are many factors that affect antenna pointing accuracy, such as the quantization error of phase shifter, the physical structure between units of TR, the installation position error and so on. In order to ensure the measurement accuracy of secondary radar, The pointing accuracy of the antenna must be higher than that of the radar system. In this paper, an efficient pointing error compensation scheme is developed. This scheme can not only greatly reduce the pointing error, but also save the time of correting the pointing error and the investment of personnel.