For the problems in the design of a flat part micro-assembly system, an orthogonal optical alignment mechanism was proposed to realize high-precision assembly of the miniature flat class structure by a man-machine cooperation micro-assembly system, and the error of high-precision alignment mechanism module was analyzed and calculated. Then, a micro-assembly system platform based on the microscopic machine vision and orthogonal optical alignment was established, and the micro-assembly experiments by proposed method were carried out. The optical alignment method proposed was effectively used in the assembly of integrated and complex micro heterogeneous electromechanical system such as the flat structures of silicon micro-MEMS devices and non-silicon MEMS devices. The results show that the consistency and efficiency of the micro-assembly are improved and enhanced greatly, and the designed platform has good openness and portability. When the prism orthogonal alignment mechanism produces the error of 0.001°, the theoretical deviation is less than 0.98 μm and the assembly accuracy of the actual experimental micro-assembly platform is less than 5 μm.The precision meets the general assembling accuracy requirements of the miniature flat class structure.