In augmented reality, virtual reality and the metaverse, three dimensional (3D) reconstruction technologies play important roles in acquiring the content information. Among them, the structured light method has been widely used due to the advantages of high precision and not being affected by the texture of the surface material on the object. Traditional structured light 3D reconstruction mainly uses digital light processing based projectors to project coded patterns. However, the shortcomings of digital light processing projectors such as large size, high power, and high price limit their applications. Therefore, more 3D scanning systems start to use a micro-electro-mechanical system mirror as a structured light projector, which has small size, low cost, and high frame rate. In this paper, the phase-height model is proposed to complete the 3D scanning system based on micro-electro-mechanical system mirror. To deal with the noise caused by the speckle effect, anti-noise performance of three time-phase unwrapping algorithms commonly used for micro-electro-mechanical system mirror are experimentally compared. Results show that the multi-frequency hierarchical method and the negative exponential fitting method show better anti-noise capability and higher precision, while the multi-frequency heterodyne method shows poor anti-noise performance. This study provides a guide in choosing proper phase resolution method for micro-electro-mechanical system based 3D scanning systems.