In order to solve the mechanical positioning error of sub-aperture in stitching interferometric measurement, we propose a mechanical error compensation method based on genetic algorithm. The algorithm uses the matching degree of sub-aperture overlapping area as the fitness function, and then uses the error search algorithm to calculate and compensate the positioning error generated in the process of sub-aperture measurement. Through simulation and experimental verification, it is proved that the algorithm can compensate the sub-aperture mechanical positioning error. The simulation results show that the angle error calculation accuracy of the algorithm is better than 0.01°, and the displacement error calculation accuracy is better than 0.16 mm. The stitching surface after compensation is basically consistent with the simulation surface. The experimental results of stitching measurement of an elliptical cylindrical mirror with the curvature radius of 100 m show that the mechanical error compensation algorithm proposed can effectively compensate the mechanical positioning error introduced in the process of stitching measurement, and reduce the dependence of sub-aperture measurement on the accuracy of mechanical displacement table.