To accurately locate patients in the process of heavy ion therapy for cancer, a method of coordinate unification between treatment room and the robot system of heavy ion therapy system based on the laser tracker and its supporting software Spatial Analyzer is proposed. First, we determine the coordinates of the calibration point in the flange center coordinate system by geometric fitting method. Second, the coordinate transformation between the robot flange coordinate system and the base coordinate system is accomplished by simple calculation. Finally, the transformation matrix between the treatment room coordinate system and the robot coordinate system is calculated by using the best fitting algorithm in Spatial Analyzer software. The unification of the coordinate system is completed, and the accuracy of the unified coordinate system is verified. The practical application in HIMM (Heavy Ion Medical Machine) shows that the coordinate unification method simplifies the conversion between treatment room and the robot system of heavy ion therapy system. Moreover, the calibration accuracy is good and the calibration efficiency is high. This method of coordinate unification is easy to operate in heavy ion therapy system and other industrial applications.