For the cruciform welded joints between corrugated bulkhead of duplex stainless steel plate and inner bottom of stainless (SUS) clad steel plate which have misalignment between the vertical steel plates under uniaxial and biaxial tensile loading conditions, numerical analysis of finite element method were performed with variable parameters of the loading condition, amount of misalignment, weld size and welding condition of penetration. The stress concentration factor on each weld toe of the cruciform welded joint was evaluated and the relations between the stress concentration factor and relative positional difference of weld toes on both side of inner bottom are investigated. As results, with misalignment, geometrical symmetry between weld leg shapes on both side of inner bottom is also desirable to avoid high stress concentration. In addition, for misalignment due to vertical alignment with mold line between vertical steel plates with difference in plate thicknesses, deep penetration welding is desirable to suppress stress concentration increased by its misalignment from comparison with fillet welding.