In order to improve the accuracy of the whole flexible measurement system, a compensation method based on robot was put forward. Constraint equations were constructed by using distance error model, and the actual geometric parameters of the robot were solved, and then these parameters were used in the modified kinematics model. Car body points were measured by using the modified kinematics model and compared with the distance data of laser tracker. Experiments prove that, the repeatability error of the measurement system is stable and less than 0.1 mm before and after compensation, but the absolute error of the measurement system declines from 0.6 mm to 0.3 mm and the accuracy is improved greatly.