Abstract: Aiming at solving axial scanning problem of dual photon fluorescence microscopy imaging system, fast axial scanning system based on digital micromirror device (DMD) is proposed in this paper. DMD is used for selecting optical path in this system, and lens groups with different focal lengths are placed in these optical paths to generate different changes of beam divergence angle. Then axial scanning spots with different depth are obtained after beam focused by objective lens. Axial scanning distance, scanning spot and diffraction efficiency are calculated and simulated. Results show that when scanning system adopts four modules or five modules, axial scanning distance can reach 1mm, focal length of lens in four modules and five modules is 297.3 mm and 361.47 mm respectively. Axial scanning spot varies in good linearity except marginal spot. Axial scanning frequency approaches to dozens of kilohertz. This scanning system can meet requirements of cranial nerve imaging.