In the GNSS-challenged/denied environments, compared with other aided navigation systems, synthetic aperture radar- (SAR-) aided navigation systems can achieve all-weather, all-day, and global positioning. This paper is aimed at designing a reliable navigation system for the supersonic vehicle in the whole flight phase. Considering the SAR is of great significance for the reliable and precise navigation of the supersonic vehicle, we introduce it to the terminal phase to cope with the interference of the global navigation satellite system (GNSS). At the same time, to accelerate the speed of SAR positioning, a positioning method based on the area feature and stack sequential decoding algorithm (SSDA) is designed. Then, applying the SAR positioning under the framework of the Kalman filter (KF), we propose a tightly coupled strapdown inertial navigation system (SINS)/SAR/GNSS integration algorithm, which can achieve positioning without a complicated fusion method between the front phase and terminal phase. The flight experiment results show that the proposed method can correct the average position error to 1.7 m within 1 cycle.