In this paper a novel constraint calibration technique for Stewart platform based Parallel Kinematics Machine(PKM) is presented. A commercial trigger probe and a developed double-ball bar gauge are employed to aid the calibration. In the measuring process the characterized errors can be obtained by comparing the nominal characterized size calculated by the function using the measuring data with the real size of the double-ball gauge. An optimization approach is used to calculate the PKM structural errors, and these errors can be finally compensated into the control model. The error transferring matrix with regard to the structural error of PKM can be formulated. The calibration efficiency can be improved by the automatic calibration operation with the doubleball bar gauge. The developed calibration system has been applied in the industry where the PKM is used for machining the turbine vane, and the machining quality can meet the requirements of the specifications. The presented calibration scheme is generic to be applied for the wide range of PKMs.