In order to modify the pointing error of three-axis optoelectronic tracking systems, a new method based on the optical-mechanical structure of three-axis systems was proposed. Firstly, related equations which show the impaction of axis errors to the pointing error of spatial target were analyzed based on the rotation transform theory of quaternion. Then, a new modification model of three-axis optoelectronic tracking system was obtained thought all the different equations. Experimental results show that the method can reduce the pointing error effectively, and the exterior-error modified capability of this method is higher than spherical-function modification model. At the same time, the method would have a certain reference guide to estimate the pointing precision during assemblage and debugging.