A new acoustic positioning method for Autonomous Underwater Vehicles (AUV) that uses a single underwater hydrophone is proposed in this paper to solve problems of Long Baseline (LBL) array laying and communication synchronisation problems among all hydrophones in the traditional method. The proposed system comprises a Strapdown Inertial Navigation System (SINS), a single hydrophone installed at the bottom of the AUV and a single underwater sound source that emits signals periodically. A matrix of several virtual hydrophones is formed with the movement of the AUV. In every virtual LBL window, the time difference from the transmitted sound source to each virtual hydrophone is obtained by means of a Smooth Coherent Transformation (SCOT) weighting cross-correlation in the frequency domain. Then, the recent location of the AUV can be calculated. Simulation results indicate that the proposed method can effectively compensate for the position error of SINS. Thus, the positioning accuracy can be confined to 2 m, and the method achieves good applicability. Compared with traditional underwater acoustic positioning systems, the proposed method can provide great convenience in engineering implementation and can reduce costs.