In digital lithography illumination system, 365 nm light emitting diode (LED) is designed by using fly’s-eye lens. The lens is arranged in a nearly hexagon array structure, which can basically cover the circular light. The nearly hexagon array can reduce the number of invalid lens compared with the traditional square structure, and the lens can be more effectively used to develop uniform light efficiency. The illumination systems with nearly hexagon array and 9×9 square fly’s-eye lens array are simulated respectively by software, and their irradiance maps are compared. Results show that the illumination system with nearly hexagon array is more uniform. The illumination system designed with the nearly hexagon array is combined with digital micro mirror device(DMD) and lithographic lens, and a digital lithography experiment with 2 μm precision is carried out. It’s found that the image surface illumination is uniform and line is clear.