When an industrial robot is operational continuously in industrial field, the position of the end effector would drift. Using external high-precision measurement system to get the accurate 3D position coordinate of the end effector is an effective method of compensating the absolute positioning error of the robot. The measurements required efficient, high-precision and adaptability, to deal with these problems, in this paper, an error compensation method of industrial robot based on workspace measurement and positioning system is proposed. Based on the dynamic performance of the system, a meshing strategy for robot workspace is designed. The grid edge length could be adjusted according to the actual distribution of positioning errors. After collecting the absolute positioning error vector values of grid nodes, for the interpolation calculation of the position error vector at key trajectory nodes, the inverse distance weighting algorithm is studied to realize the compensation of the position errors of the end effector. The experimental results exhibit that after installing 20kg load, the average absolute positioning error of the robot is reduced from 1.36mm to 0.19mm, the absolute positioning accuracy of the robot is improved by about 86% after compensation. It indicates that this proposed high-efficient method can significantly improve the site operation accuracy of the industrial robot.