In three-dimensional (3D) shape measurement based on phase measuring, the ultimate and important job is to map the phase to height and map the image coordinates to the global ones, which are usually done by 3D calibration. It’s a key process because of its relation to the accuracy of the measurement. Based on the dual-direction nonlinear phase-height mapping technique and the Pinhole camera model without lens distortion, and considered the characteristic of Fourier spectrum of a linear structured signal, a method which can complete the calibration of height (Z) and the lateral coordinates (XY) simultaneously by orientation filter is presented. The method has been used successfully to calibrate the system of rotating blade measurement, its standard deviation is less than 0.27 mm in the lateral coordinates (230 mm× 230 mm) and 0.022 mm in height (72 mm). 3D calibrations can be easily and perfectly done with the method.