A novel positioning error compensation method (PECM) based on the measured and target position error for multiple degrees of freedom (DOF) robot arm control is proposed, which is used to improve positioning accuracy of multiple-DOF robot arm end-effector in accurate positioning applications such as in the medical and mechanical fields. Based on the idea of PID to increase adaptiveness and robustness of the method, a positioning compensation model between the measured and target position error tracked by an optical tracking system and compensated joint angle is derived with inverse kinematic model. Based on error analysis of the compensation model regarding geometry errors, the proportional joint angle compensated coefficient deduced from Jaccobian matrix of the error is proposed and identified with position error data. Calibration experiments for position conversion matrix and positioning accuracy verification experiments are conducted consisting of an optical tracking system and a robot arm. The results of positioning accuracy verification experiments show that the average resultant positioning error in three directions reduces from 1.89 mm (before compensation, model based on Denavit-Hartenberg (DH)), 0.39 mm (model based on modified Denavit-Hartenberg (MDH) with Levenberg-Marquardt (LM)) to 0.34 mm (decreasing 82%, 15%), which demonstrates the efficiency and robustness of the method.