A residual stress generated in the steel structure is broadly categorized into initial residual stress during manufacturing steel material, welding residual stress caused by welding, and heat treatment residual stress by heat treatment. Initial residual stresses induced during the manufacturing process is combined with welding residual stress or heat treatment residual stress, and remained as a final residual stress. Because such final residual stress affects the safety and strength of the structure, it is of utmost importance to measure or predict the magnitude of residual stress, and to apply this point on the design of the structure. In this study, the initial residual stress of steel structures having thicknesses of 25 mm and 70 mm during manufacturing was measured in order to investigate initial residual stress (hereinafter, referred to as initial stress). In addition, thermal elastic plastic FEM analysis was performed with this initial condition, and the effect of initial stress on the welding residual stress was investigated. Further, the reliability of the FE analysis result, considering the initial stress and welding residual stress for the steel structures having two thicknesses, was validated by comparing it with the measured results. In the vicinity of the weld joint, the initial stress is released and finally controlled by the weld residual stress. On the other hand, the farther away from the weld joint, the greater the influence of the initial stress. The range in which the initial stress affects the weld residual stress was not changed by the initial stress. However, in the region where the initial stress occurs in the compressive stress, the magnitude of the weld residual compressive stress varies with the compression or tension of the initial stress. The effect of initial stress on the maximum compression residual stress was far larger when initial stress was considered in case of a thickness of 25 mm with a value of 180 MPa, while in case of thickness at 70 mm, it was 200 MPa. The increase in compressive residual stress is almost the same as the initial stress. However, if initial stress was tensile, there was no significant change in the maximum compression residual stress.