The invention provides a welding method for reducing the site-welding stress deformation of a thick-walled steel structure, and relates to a welding method. The problems that for an existing steel structure, adjustment of welding residual strain to a welding process is passive, cumbersome and difficult, and the structure of welding joints is poor in stability and anti-fatigue performance are solved. The method comprises the steps that multiple inlaid internal webs are arranged at welding grooves of welding groove at intervals in the length direction of a welding seam, wherein a skeleton systemstructure is jointly formed by welding groove walls of base materials and the inlaid internal webs; welding of the internal webs is conducted, wherein back gouging welding is adopted to ensure complete fusion between the internal webs and the base materials of the welding groove walls of the butt joints; and after the skeleton system structure of the butt joints is welded and formed, filling welding is conducted on a partition space formed by the welding groove walls of the base materials and the multiple inlaid internal webs in an enclosing manner, and cover surface welding is conducted in the longitudinal welding direction of the welding seam. The welding method is used for reducing the site-welding stress deformation of the thick-walled steel structure.