When using a fly’s eye lens system to homogenize highly coherent light sources, the interference effect between the sub-beams can cause a periodic speckle distribution of illumination intensity, thereby disrupting illumination uniformity. It has been shown that using a rotating optical phase-shift plate behind the fly’s eye lens can eliminate interference patterns, but it only demonstrates engineering realizations. And the theoretical analysis and technical guidance on the phase modulation method and statistical averaging method for fly’s eye lens homogenization systems are still lacking. In this work, a simulation model of fly’s eye random phase modulation homogenization system is developed and studied in detail. Each sub-beam of the fly’s eye lens is randomly phase-modulated to break the coherence condition, and the illumination intensity of multiple independent modulations is accumulated to eliminate the interference pattern. The more times the intensity is accumulated, the better the homogenization is. Meanwhile, studied in this paper are the influence of the diffraction effect on homogenization, and the influence of the sub-lens size and focal length on the homogenization, which result in the diffracting-type system and the imaging-type system respectively. For an imaging type system, it is necessary to ensure that the first fly’s eye lens is in the front focal plane of the second fly’s eye lens. By optimizing the parameters of the fly’s eye lens and using an imaging-type system with p= 1.8 mm and f _A= 9 mm, a Gaussian beam with the non-uniformity of 117% is homogenized into a flat-topped beam with the non-uniformity of 1.2% in a square illumination area of 100 mm ². This fly’s eye lens random phase modulation homogenization system has a simple structure, low energy loss, and good illumination uniformity, and can be used in systems that require high coherent laser input and high resolution. This technology can be used in the field of deep-ultraviolet mask defect detection.