For 351 nm XeF excimer, an illumination system for PCB laser projection image used for high resolution, high throughput, large area and conventional photoresists exposure is designed. On the basis of the theory model of the excimer’s partly coherent flat-top Gaussian beam (PCFGB), the diffractive characteristic of micro-lens array (MLA) homogenizer is theoretically analyzed. The uniformity of MLA homogenizer influenced by the diffractive effect is quantitatively analyzed by means of distribution of PCFGB, diffractive angles of constant intensity and Fresnel-Kirchhoff diffractive integral formula. The theoretical calculation indicates that the amplitude is modulated not only by Fresnel diffraction at the microlenses edges but also by multiple beam interference, and it is just obvious that the spikes produced by diffraction emerge in the beam edges. Meanwhile, for the PCFGB curves obtained by numerical integral, it is found that 9×9 MLA homogenizer can ensure the overlapping uniformity of the beams from individual microlenses and decrease the effect of the diffraction and multiple beam interference to a great extent. By way of using a hexagonal diaphragm, the spikes at the beam edges produced by diffraction can be cut down and the large-area seamless scanning lithography met. Using ZEMAX optical design software to simulate the effect, it shows that the process window is less than ±2%。