The periodic micro-pillars on the hard-brittle fused silica surface can be shaped into the smooth and defect-free microlens arrays (MLA) by CO2 laser polishing, which can be applied in imaging and beam-shaping. However, the morphology evolution mechanism of the micro-pillars is not clear during polishing, which seriously affects the rapid preparation of high-quality MLAs. Herein, a multi-physics coupling model is established to investigate the interaction between CO2 lasers and micro-pillars on the fused silica surface, and is verified from the perspectives of temporal and spatial temperature. The steady surface temperature evolution law with laser power and spot radius is explored, based on which, the parameter ‘Window’ for polishing is determined to make the material melt and flow without ablation removal. The morphology evolution of micro-pillars is investigated as well as laser-material interaction. It is found that under laser irradiation, the micro-pillar height first increases and then decreases, and its top curvature radius increases. The surface tension makes the dominant contributions to the melting and flow of the micro-pillar materials, while the Marangoni effect and the gravity have little effect. Furthermore, to fabricate the target MLAs with the specific dimensions, the influence of micro-pillar aspect ratio (φ) on microlens surface morphology is investigated. It is found that there are two critical φ for the target MLAs. For the required MLA with the target period of 200 μm and the target height of 40 μm, when the φ is larger than 5.1, the micro-pillar array fails to be shaped into the target MLA by CO2 laser polishing. As the φ decreases, the junction of micro-pillar and the substrate sags downwards significantly, and the deviation between the shaped- and the ideal spherical contours increases. To successfully prepared the target MLA and guarantee the geometry accuracy, the minimum φ is selected to be 0.71. This work has important theoretical significance for obtaining the smooth and defect-free target fused silica MLAs with the specific dimensions by CO2 laser non-evaporative polishing.