In view of many uncertainties in the complex fatigue process of actual structural members, fatigue reliability analysis is needed to quantify structural safety assessment. Compared with thick plates, thin plate welded joints are more prone local deformation and global angular deformation, which seriously affects stress concentration effect and fatigue performance at welded corners. With the increasing importance of lightweight structure, both the initial local deformation and the global angular deformation of thin plates should be considered in fatigue reliability analysis. The limit state equations of three typical welded joints (butt joint, T-shaped and cross-shaped) were constructed based on the renewed critical stress amplification factor method to consider the initial deformation of thin plate joints. Moreover, considering the existing experimental data and the tolerance of welding deformations recommended in codes, the fatigue reliability was re-evaluated by JC method for thin plate welded joints. The results show that the reliability indexes of thin plate welded joints are closely related to the plate thickness, and the tolerance recommended by the traditional code should be corrected for the plate thickness. Therefore, considering the initial welding deformation, this paper quantitatively calculates the lateral deformation limit of typical welded joints, and presents the results of lateral deformation limit under different reliability indexes.