It is very important that sub-assembly structures such as transverse web, floor, girder, etc. are built more accurately as designed, in order to reduce working man-hours and to introduce automated machines at assembly and erection stages. To achieve more accurate assembling of the parts, reasonable and quantitative estimation of welding deformation is essential, since many stiffeners and tripping brackets are welded, which are generally arranged transversely to the web length. In this paper, shrinkage of the web plate by fillet welding of the stiffener is discussed experimentally, because the shrinkage affects total length of the sub-assembly member. Some series tests using structure models of unit breadth-1 stiffener space-were carried out by measurements of thermal distribution and displacement of the plate, in cooperation with FEM calculation. As a result, effect on the shrinkage is investigated parametrically, and estimation formulas are proposed for mild steel and high tensile steel currently applied, based on the heat input of weld and the plate thickness. In addition, metallurgical characteristics of the steel at higher temperature condition are also studied experimentally.