Laser ablation is widely used as a flexible and non-contact processing technology for the fabrication of fused silica. However, the introduction of thermal stress inevitably leads to crack growth and reduces the lifetime of fused silica. Due to the complicated coupling interaction and properties of fused silica, the unclear thermal stress formation is the bottleneck restricting further development of laser ablation. In this article, a three-dimensional multi-physics thermo-mechanical model was developed to reveal the evolution mechanism, and experiments were performed to validate the simulated results. The surface morphology evolution was elaborated during process cycles, with recoil pressure identified as the key factor in determining surface morphology. Moreover, thermal stress was quantified utilizing optical retardance and stress birefringence, effectively distinguishing between non-thermal and thermal stress induced by laser ablation. The theoretical simulations fit well with experimental measurements. Meanwhile, stress distribution and evolution behaviors were revealed under different processing parameters by this model. This work not only contributes to a profound understanding of the laser ablation process but also establishes a theoretical foundation for achieving high surface quality and non-thermal stress laser ablation.