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In this paper, we introduce a novel sub-bottom profiler, making good use of the Mills cross configuration of multibeam sonar and synthetic aperture techniques of the synthetic aperture sonar system. The receiver array is mounted along the ship keel, while the transmitter array is mounted perpendicular to the receiver array. With the synthetic aperture technique, the along-track resolution can be greatly improved. The system often suffers from motion error, which severely degrades the imaging performance. To solve this problem, the imaging algorithm with motion compensation (MC) is proposed. With the presented method, the motion error is first estimated based on overlapped elements between successive pulses. Then, the echo data is processed by using the range migration algorithm based on the phase center approximation (PCA) method, which simultaneously performs the MC with the estimated motion error. In order to validate the proposed sub-bottom profiler and data processing method, some simulations and lake trial results are discussed. The processing results of the real data further indicate that the presented configuration has great potential to find buried objects in seabed sediments.