The design and fabrication of the ultra-miniature microlens array homogenizer using two-photon polymerization is presented in this paper. The flat-top laser beam shaper includes refractive type, diffuser type and microlens array homogenizer. The drawback of the refractive and diffuser type is that the uniformity on the homogenization plane is associated with the laser Gaussian beam profile. However, the microlens array homogenizer is independent of laser beam profiles. Therefore, the microlens array is employed for the laser beam shaper in this study. In the simulation, the incident Gaussian elliptical laser beam is successfully transformed into a homogenized rectangular distribution by the microlens array homogenizer. Because the flat-top beam distribution is in the range of micrometer (μm) level in this study, the pitch of the microlens array is reduced to tens of microns, which is not suitable for general machining. Therefore, 3D printing using two-photon polymerization fabrication without tool interference issues is utilized. Finally, the microlens array homogenizer is successfully fabricated. The ultra-miniature flat-top laser beam shaper can accomplish a uniform rectangular distribution of 220 μm X 300 μm, which can be applied for high precision applications such as laser processing, laser medical, and laser display.