Abstract: The influence of welding thermal effect on the dynamic performance of complex structure was proposed and confirmed by both formula derivation and numerical solution by finite element analysis method. Based on constitutive relation including initial stress and strain,the stiffness matrix considering the welding thermal effect was derived by employing the principal of virtual work. Then modified characteristic equation of modal analysis including geometric non-linear,stress stiffening and welding thermal effect was established. Modal analysis by taking a ship hull block as the example was performed to testify the derived equation and the first natural frequencies were extracted. The comparisons of different first natural frequencies induced by different levels of welding residual stress exhibited that the welding thermal effect obviously influenced the vibration performance of hull block by changing natural vibration frequencies of the structure. Especially,certain value of welding residual stress could even lower the first natural frequency nearly to wave frequency. The results show that the welding thermal effect played an important role in the dynamic performance of structure and could not be neglected in vibration analysis.