In order to reveal the evolution mechanism of repaired morphology and the material’s migration mechanism on the crack surface in the process of CO2 laser repairing surface damage of fused silica optics, two multi-physics coupling mathematical models with different scales are developed, respectively. The physical problems, such as heat and mass transfer, material phase transition, melt flow, evaporation removal, and crack healing, are analyzed. Studies show that material ablation and the gasification recoil pressure accompanying the material splash are the leading factors in forming the Gaussian crater with a raised rim feature. The use of low-power lasers for a long time can fully melt the material around the crack before healing, which can greatly reduce the size of the residual air layer. Combined with the experimental research, the methods to suppress the negative factors (e.g., raised rim, deposited debris, air bubbles) in the CO2 laser repairing process are proposed.