CO2 laser polishing process is a highly effective way for enhancing the surface quality and laser-induced damage threshold of fused silica optics. Nevertheless, due to the thermal history and spatial gradient of the thermodynamic temperature, the heat-affected zones can be formed unevenly on the surface with an increased fictive temperature, which causes the material densification and residual stress. In this work, a 3D model of structural relaxation coupled with temperature and flow fields was innovatively established to explore the role of fictive temperature distribution involved in CO2 laser polishing of fused silica. The Raman spectrum was applied to verify this model. Subsequently, the impacts of laser beam power, scanning speed, track overlapping, substrate temperature on the fictive temperature were discussed. The results indicate that decreasing the scanning speed and increasing the substrate temperature can decrease the fictive temperature. Additionally, a higher track overlapping can reduce the height of the fictive temperature “tool mark”. Moreover, an optimization strategy based on laser beam scanning speed was proposed based on the uniform distribution of fictive temperature. The depth difference of the heat-affected zones was reduced from 164.26 μm to 31.74 μm. This work could be used to quantitatively predict the 3D fictive temperature distribution and proposed an optimization strategy based on scanning speed to suppress the non-uniformity of fictive temperature distribution, which can provide significant theoretical guidance for CO2 laser polishing technology of fused silica optics.