Due to the coherence of laser light source it could produce coherent noise in parallel confocal microscopy based on Digital Micromirror Device (DMD) and thus affect the resolution. LED light source instead of the laser light source can give full play because of its incoherence characterization. In this paper, free-form surface lens is used for LED secondary optics design. According to the LED characteristics and the law of refraction, we have established differential equations of free-form surface. We solved equations with the method of Runge-Kutta by Matlab and the model was built in Tracepro for optical simulation. The results show that the uniformity on the DMD is better than 90% and the lighting efficiency is higher than before. The measured data show us a much more uniform illumination on DMD and LED uniform illumination system successfully avoided the gray error which was caused by the uneven illumination. The LED driver circuit using DC power supply provides us a more stable light source. The axial optical tomography is more accurate and the reconstruction of three-dimensional image is more clearer.