The basic imaging formula of the fly-eyes illumination system has been deduced from the optical imaging point, according to the characteristics of LED emission and the characteristics of the Color-Filter Liquid Crystal on the Silicon(CF-LCoS). The initial lighting system of the CF-LCoS can be given with the basic formula of the fly-eyes imaging system by considering the size of the target area of the CF-LCoS , the incident angle of the light beam on the CF-LCoS , the requirement of the spot size and the divergence angle after LED′s light shaping. Then with the multi-conjugate imaging relationship of the fly-eyes illumination system, the fly-eyes imaging and the relay lens imaging can be optimized, which can be linked up to form a fly-eyes and the illumination system of the CF-LCoS under large illumination angle through the matching principle of the aperture and the intermediate image finally. The problem of lighting system efficiency, uniformity and large incident angle can be solved by using less number of eyes under the condition of ensuring the illumination requirements of the CF-LCoS. This method is simpler and more accurate than the traditional calculation method. The simulation results of the non-imaging software show that the illumination is with good uniformity and high efficiency. Finally, the experimental prototype is designed and fabricated to verify the correctness and effectiveness of the proposed method.