Ultra Short Baseline (USBL) navigation systems are often faced with positioning errors arising from misalignments between sensors. This paper proposes a line survey method for USBL angular alignment calibration. In the scheme of USBL line survey, mathematical representations of positioning error arising from heading, pitch and roll misalignments are derived, respectively. The effect of each misalignment angle and how the differences can be used to calibrate each misalignment angle in turn are presented. An iterative algorithm that takes advantage of the geometry of position errors resulting from angular misalignments is developed for USBL calibration. Numerical simulations are provided to demonstrate the effectiveness of the USBL line survey approach. In addition, the effect of measurement error on the estimation of roll alignment error is evaluated and discussed.