Ultra-short baseline (USBL) underwater positioning systems are widely used in marine scientific research and ocean engineering. Angle misalignment is a main error that reduces the accuracy of USBL underwater positioning. The conventional angle-calibration method assumes that the transponder position obtained by USBL positioning is an errorless coefficient matrix. However, errors inevitably exist in the estimation of the transponder’s position via USBL positioning, and the precision varies at different epochs. Ignoring the error in the transponder’s position will significantly reduce the precision of the angle misalignment estimation. In this paper, a new angle-calibration method is proposed for precise USBL underwater positioning. The angle alignment model is derived by treating the transponder’s position obtained by USBL positioning as an observation, and the stochastic model is then established according to the bearing angles. Robust estimation is likewise applied to further improve the precision of the angle misalignment estimation. To verify the performance of the proposed method, a sea experiment was performed. The results show that the new method has high calibration accuracy and robustness. The estimation precision of this method is improved by 0.0457°~0.6896° in heading, 0.0125°~0.8072° in roll, and 0.0077°~0.9436° in pitch, compared with that of the conventional angle alignment method.