In view of the increasing demand for various kinds of high orbit aircraft navigation, a navigation method is proposed for high orbit specific targeted aircraft. The method requires a full digital phased array antenna and a high gain navigation antenna with a tunable high gain antenna in the navigation satellite. Phased array antenna receives the signal of target vehicle launched for the Direction of Arrival(DOA) analysis and estimates the signal DOA, as well as the direction of the aircraft relative to its own by the multiple navigation satellites. Based on this direction, the navigation satellite can adjust its high gain navigation antenna and make it point to a specific target aircraft, and transmit the navigation message, so as to realize the navigation task of the high orbit spacecraft. In this paper, the navigation satellite phased array antenna is assumed to have the visibility of the satellite phased array antenna on the surface of the satellite. Based on the target, the accuracy of the two dimensional DOA estimation is calculated. The feasibility of the method is verified.