During the welding of the wall plate of cylindrical structure, the edges of cylinder generates obvious wave-like deformation and affects subsequent assembly. In this paper, based on the numerical simulation method, welding deformation controlling by pre-stress method is studied. The effects of the pre-stress level and the welding sequence on the final deformation are discussed. The results show that the level of pre-stress can obviously control the welding deformation of the longitudinal beams, but can not control the welding deformation of transverse beams. Using the selected welding sequence: welding transverse beams firstly, exerting pre-stress, and then welding longitudinal beams, this welding sequence can reduce the wave-like deformation after welding.