With the development of aviation industry, more stringent demands are put forward for the performance and manufacturing level of aircraft. Moreover, the automation and precision of aircraft assembly determine the efficiency and quality of aircraft production. In order to improve the positioning precision of the flexible track hybrid robots which are applied to the flexible automatic assembly of aircraft, a precision compensation method based on response surface methodology was proposed in this paper. Firstly, the global positioning error model, optimized by characteristics of error data, was constructed to predict the positioning errors of the flexible track hybrid robot. Secondly, the predicted errors are utilized to realize the compensation of the target points at drilling workspace on nose and front fuselage assembly areas. Finally, a series of experiments of the flexible track hybrid robot with no-load and drilling scenarios are implemented to validate the proposed precision compensation method. The experiment of a hybrid robot for aircraft assembly shows that the mean value of the absolute positioning precision of the end-effector was promoted from 0.081 mm to 0.025 mm, maximum error reduced from 0.143 mm to 0.039 mm., respectively, which means that the position accuracy of the robot is increased by 69.1% and 72.7% for two experimental conditions.