The web-to-stiffener weld was subjected to bending-shear action, which was always neglected in previous research and affected the accuracy of fatigue evaluation. In this study, multi-scale FEMs (finite element models) of steel plate girder bridges were established to investigate the deformation characteristics, thus revealing the generating mechanism of bending-shear action. The fatigue comparison tests under bending-shear load and bending load were conducted to identify the cracking mechanism and its impact. The stress characteristics at the weld end were further explored through the structural mechanical model and verified by FEMs. The results show that the bending-shear action was caused by the inward and downward pulling by the stiffener on the web, and would lead to a premature transition from fatigue cracking to brittle fracture. The ratio of shear stress to normal stress was independent of load, inversely proportional to gap height, and positively related to web thickness, which could provide support for the accurate fatigue evaluation of web-to-stiffener weld.