In this paper, we propose and experimentally demonstrate a three-dimensional (3D) microscopic system that reconstructs a 3D image based on structured light illumination. The spatial pattern of the structured light changes according to the profile of the object, and by measuring the change, a 3D image of the object is reconstructed. The structured light is generated with a digital micro-mirror device (DMD), which controls the structured light pattern to change in a kHz rate and enables the system to record the 3D information in real time. The working distance of the imaging system is 9 cm at a resolution of 20 μm. The resolution, working distance, and real-time 3D imaging enable the system to be applied in bridge and road crack examinations, and structure fault detection of transportation infrastructures.