To investigate the fatigue performance of typical rail vehicle body base material butt joints and the regulatory effect of welding methods on them, this study uses two commonly used body materials—Q310NQL2 (plate thickness 2 mm) and Q355ME (plate thickness 3 mm)—as research subjects. Four sets of butt joint specimens were prepared using laser welding and arc welding processes, followed by tensile and fatigue performance testing. First, tensile tests determined fundamental mechanical parameters including elastic limit, yield strength, ultimate strength, and conditional fracture strength for each joint group. These values established the initial stress level for fatigue testing. Subsequently, the fatigue limit under various survival rates was tested and calculated using the step-up method, and compared with the DVS1612 standard for analysis. Results indicate that under identical material and thickness conditions, welding method significantly influences the fatigue limit of butt joints. At equivalent survival rates and confidence levels, arc-welded joints generally exhibit higher fatigue strength than laser-welded joints. Further investigation reveals that when the survival rate increases from 95% to 99.5%, the fatigue limit of both joint types shows a pronounced downward trend. This pattern aligns with theoretical expectations that higher survival rates lead to increased dispersion in fatigue data and greater conservatism in engineering design.