Parallel light exposure machine with large area is an important manufacturing equipment for electronic products such as printed circuit board (PCB), display panel, touch screen, and so on. Due to the use of non-axisymmetric Kohler illumination light path with fly-eye lens and a mirror, the uniformity of the exposure machine is only about 0.85, which cannot meet the needs of high-precision machining. Aiming at this problem, a fly-eye lens with free-form surface is proposed to replace traditional spherical fly-eye lens, and a free-form surface design method of high-uniformity fly-eye unit is established. The experimental results of ray tracing simulation analysis show that the exposure uniformity is improved to more than 0.91 by using the proposed method, which can meet the needs of high-precision machining. The designed fly-eye lens with free-form surface, which has continuous surface and can be machined by diamond turning, is expected to be widely used in the illumination path of parallel light exposure machine with large area.