Microlens arrays (MLAs) made from fused silica possess broad applications in wavefront sensing, optical focusing, beam shaping, etc. However, it is challenging to fabricate the hard-brittle silica MLAs with high accuracy and low cost by conventional manufacturing techniques efficiently. In this work, a novel two-step method, which consists of rapid evaporative ablation and precision melting polishing by CO2 lasers, is proposed to fabricate high-quality MLAs. The first step is to rapidly ablate and engrave micro-pillar arrays (MPAs) with flat groove bottom by high-energy density CO2 lasers. The second step is to precisely polish and shape the flat-topped MPAs into the dome-topped MLAs with good surface roughness (Sa) by low-energy density CO2 lasers. The whole preparation process could be achieved through a set of machining system. Firstly, the geometric dimension (period, p and height, h) of the microlens is determined by the Monte Carlo ray tracing method. Secondly, to diminish the groove depth inconsistency caused by heat accumulation, the multiple ablation compensation strategy is developed. The MPAs (p = 200–400 μm), of which maximum height error is 7.1%, are prepared in 1 s by the proposed compensation strategy. Then, the MPAs are smoothed into the MLAs by low-energy density CO2 lasers, and the average Sa is improved from 960 nm to 32.56 nm. Finally, the optical performances of the MLAs are verified from the effectiveness of imaging, focusing and homogenization. The proposed two-step processing method paves a new way to fabricate high-performance MLAs on hard-brittle fused silica with low cost and high efficiency.