This study investigated how welding affects the thermal deformation of square cells produced for casks, which are dry storage containers for spent nuclear fuel. We aimed to minimize structural deformation by utilizing STS316L as the material for the square cells. We explored a method of subdividing the square cells and joining them through butt welding. Keeping the upper plate thickness constant, GTA butt welding was conducted while varying the column’s wall thickness, followed by measurement with a laser vision sensor. The heat conduction and thermal strain were then calculated using a finite element analysis (FEM). Both experimental and analytical results confirmed that there was significant thermal deformation in the cases of thick-walled columns due to variations in heat conduction distribution, with the resulting deformation patterns depending on thickness.