Although no optically visible damage is produced in the fused silica under laser irradiation below its laser-induced damage threshold (LIDT), defect proliferation may occur due to the evolution of its internal atomic structure. The escalation in defect content leads to heightened absorption, and resulting in the degradation of the optical performance of the optics. In recent decades, there have been a lot of experimental studies on laser-induced damage and laser conditioning, but there is still a great lack of in-depth understanding and theoretical analysis of the evolution process of point defects in fused silica. In this study, the emphasis is on the evolution of point defects and fatigue damage in fused silica under multi-pulse nanosecond laser irradiation. To address this, a point-defect evolution model is developed, and the coupled evolution law of temperature and defect during laser irradiation is derived by integrating it with a numerical model. The results demonstrate that the model effectively predicts the defect evolution of fused silica under laser irradiation and facilitates the prediction of fatigue damage. It is revealed that the rate of defect evolution in fused silica is more influenced by temperature than stress, and a temperature threshold can be used to judge the condition of damage occurrence. Furthermore, through an analysis of the effect of laser fluence on defect relaxation rate, a defect relaxation method employing variable laser fluence was proposed. This study provides a reliable theoretical analysis method for understanding the fatigue damage induced by multi-pulse laser irradiation in fused silica and offers a new perspective for the annealing treatment of point defects in fused silica.