Abstract: Combining fringe projection profilometry and stereomicroscope, a system is setup which can measure three-dimensional topography of micro devices. This system consists of Greenough-type stereomicroscope, projector, CCD camera and mechanical translation table. After unambiguous phase is obtained by using phase shift algorithm and descrambling method, which is modulated by surface topography, height value is obtained by phase and height mapping relationship, so that surface morphology of micro devices can be reconstructed. At the time of calibration, ceramic calibration plate is set at different heights by means of a precision mechanical translation table, and several groups of corresponding phase and height values are obtained. Then polynomial fitting of each pixel is performed to determine phase-height mapping. Last calibrated plane and micro ball grid array are measured. Results show that measurement error is within 10μm, and spherical structure is clearly seen from three-dimensional reconstruction of micro-ball grid array. It is proved that system can accurately measure both planar and complex three-dimensional structures.