As the demand for industrial inspection continues to increase, structured light 3D reconstruction technology is increasingly developing towards miniaturization and high precision in the field of industrial inspection. Aiming at the disadvantages of the small field of view and close-range detection systems, such as high cost, large size and heavyweight, a set of low-cost, high-precision, and high-resolution 3D reconstruction system suitable for measuring small objects with structured light is designed. In this paper, a microscope structured light system which composed of a USB camera and a MEMS programmable projection module with advantages that low-cost, high-accuracy, and high-resolution was proposed. A four-step phase-shifting algorithm and multi-frequency heterodyne algorithm are applied to decode the absolute phase value. Finally to calculate the 3D coordinate by using the correspondence between the absolute phase value and the actual 3D object point (The correspondence can be acquired by system calibration). Experiments show the accuracy of the system can achieve 4\(\mu \)m, and the measuring height range is 1.5 mm. Summarily, this system could greatly satisfy the requirement for the high precision 3D reconstruction of the micro parts.