When fused quartz substrates are irradiated by high energy laser, the thermal deformation caused by heating would deteriorate the beam quality emitted by the system. In order to study the deterioration of beam quality, COMSOL finite element analysis software was used. The thermal deformation analysis model of fused quartz substrates irradiated by continuous high energy laser was established. The thermal deformations of the substrates under different clamping modes were compared and analyzed. The temperature distribution and deformation distribution of the substrate after heating were obtained. The effect of thermal deformation of fused quartz substrates on beam quality was quantitatively analyzed by VirtualLab software. The results show that, the thermal deformation is the smallest in boundary fixation. The thermal deformation of the substrate will affect the beam quality. The longer the laser irradiation time, the greater the thermal deformation, the greater the impact on the beam quality. When the substrate is irradiated by laser for 20s, the maximum deformation of the substrate of splint fixation is 415.90nm. The beam quality factor is deteriorated from 1.0036 to 1.4571. The maximum deformation of the substrate of boundary fixation is 98.38nm. The beam quality factor is deteriorated from 1.0036 to 1.0064. This result has important guiding significance for the subsequent laser beam combining system construction and beam quality optimization.