Autonomous underwater vehicles (AUVs) are important tools for exploring and studying the ocean. To improve the stealthiness of AUV positioning, a new type of inverted ultra-short baseline (i-USBL) positioning system is proposed in this paper. The system uses a surface GPS buoy as a positioning base station to transmit positioning signals to the AUV, which receives the signals through the i-USBL and calculates its own coordinates. In this way, the power consumption of the AUV will be lower, improving its endurance. In addition, azimuth observation is one of the key observation quantities in ultra-short baseline positioning systems. Therefore, this paper derives two phase difference estimation algorithms for azimuth measurement, which are the Least Mean Square (LMS) algorithm and the Discrete Fourier Transform (DFT) algorithm. Simulation results show that when the signal-to-noise ratio (SNR) is less than or equal to 0 dB, the DFT algorithm has higher accuracy; when SNR is greater than or equal to 10 dB, LMS has slightly higher accuracy than DFT; however, DFT is more stable than LMS at all SNRs. When SNR is 20 dB, the maximum azimuth measurement error of LMS and DFT is 0.3301° and 0.2204°, respectively, which can meet the positioning accuracy requirements. The average running times of LMS and DFT are 0.085 s and 0.011 s, respectively, and LMS has a faster running speed. In summary, the LMS algorithm can be used for azimuth observation when the SNR is good, and DFT can be applied when the SNR is poor.