At present, the articulated arm coordinate measuring machine is playing more and more important role in industrial production. But due to its special structure, the small change of the joint angle can cause large measurement error. So the calibration of the angle variable error can effectively improve the measurement accuracy of the articulated arm coordinate measuring machine. In order to realize the direct calibration of the articulated arm coordinate measuring machine’s perpendicularity error, the two symmetric point method was put forward. Firstly, the mathematical model of the articulated arm coordinate measuring machine was established and the kinematics equation was obtained. Secondly, the perpendicularity error calibration principle was analyzed and the perpendicularity error calculation formula was obtained. Finally, with the help of the mechanical fixture, the experiments were carried out on the ROMER Infinite 2.0 articulated arm coordinate measuring machine. The accuracy of the calibration results was verified by the measurement experiment of the standard ball. This method can make the measuring result of the articulated arm coordinate measuring machine relative error reduce from 0.384% to 0.225%. The calibration method can improve the measurement accuracy of the articulated arm coordinate measuring machine. This research laid a good foundation for the further research of the measurement accuracy of the articulated arm coordinate measuring machine.