In order to improve the positioning accuracy of Inertial Navigation System/Doppler Velocity Log (INS/DVL) integrated navigation system in water ships, a calibration method of installation deviation by GPS positioning information for vector calculation is proposed. This method only needs the ship to navigate two distances along different directions in a straight line, relying on the velocity information under GPS for vector calculation, and the installation deviation between INS and DVL can be calibrated. The test results show that the DVL installation deviation can be reliably calibrated by this method, and the integrated navigation accuracy can be effectively improved by substituting the calibration results into the evaluation.