In order to measure workpiece′s micro-nano three-dimensional topography, a parallel confocal microscopy detection system based on digital micromirror device(DMD) is set up. Firstly, the Fraunhofer diffraction model of DMD is studied. Secondly, the parallel scanning model of 2×2 pixel unit and T=3 is realized by the use of DMD. Then the three-dimensional image reconstruction algorithm and laser speckle homogenization is analyzed. Finally, the measuring system makes three-dimensional measurements for coated plate, WSZ position sensitive anode detector and screw respectively. The experimental results show that the three-dimensional reconstruction image is obtained under the condition that the stepping motor moves 10 nm per step. This parallel confocal microscopy system greatly improves the three-dimensional testing speed and can satisfactorily meet the general industrial testing requirement. It provides a new method of research and application for parallel confocal detection technology.