The invention discloses a method for estimating heading angle deviation between a water surface/ an underwater vehicle and a positioning device. Firstly, the vehicle performs directional straight navigation on the water surface or underwater, and at the same time, through self-positioning and positioning by use of the positioning device, discrete registration point data of the vehicle in geodeticcoordinates in the northeast direction can be obtained; self-motion track points of the vehicle and positioning device test data are fitted into straight lines by data fitting, and an angle differencebetween the two straight lines is a heading angle deviation value of the vehicle and the positioning device; multiple tests are performed in the same direction, the average of data of the multiple tests is computed to obtain the heading angle deviation of the direction; the vehicle is controlled to perform straight navigation in different directions, the above steps are repeated to obtain the heading angle deviations of the directions, and if the relative error of the heading angle deviations in the multiple directions is less than 5%, the average of the heading angle deviations in the multiple directions is computed. The method is convenient to operate, the positioning data acquired by the positioning device is more precise, and the method is suitable for various different vehicle navigation environments.