Abstract: How to accurately estimate the installation angles between the carrier and the acoustic array is one of the main factors that affect the data quality of acoustic Doppler velocity meter in the application. A joint calibration method based on the trajectory between GPS and velocity meter, the depth of velocity meter is applied to estimate the three-dimensional installation angles. Firstly, based on the characteristic that misalignment pitch β and roll γ show little impact on misalignment heading α, observation equation of α is set up with the use of high-precision GPS and attitude device on carrier, and dead reckoning. And then α is calibrated. Secondly, taking use of the geometric equation between the distance in beam space and β or γ, the exact solution can be obtained. In order to evaluate the performance of the method, the effect caused by the observation equipment is simulated. And field experiment is made to verify its effectiveness. It shows that the method effectively solves the problem of the array installation angles, which can be applied in engineering.