Abstract: Objective Aiming at the problems of limited applicability and low analysis efficiency of traditional fatigue assessment methods for welded structure in complex joints, engineering application method of structural stress method in large and complex welded structures is studied to improve accuracy of fatigue failure mode determination and life assessment. Methods A comparative analysis was conducted on fatigue assessment methods such as the nominal stress method, hot spot stress method, and notch stress method, with a focus on the study of mesh insensitive structural stress method. This paper proposed a structural stress analysis method based on shell element. Taking U-rib welded joints of orthotropic bridge decks as an example, accuracy of shell element modeling was verified by comparison with solid element model, and this method was applied to fatigue behavior analysis of butt joints with backing plates. Results The results show that structural stress obtained by shell element model is basically consistent with that of solid element model in terms of distribution law and numerical magnitude, and can accurately reflect stress concentration characteristics of welded joints. After considering angular deformation, structural stress method can reasonably predict fatigue failure position of butt joints with backing plates, and differences of fatigue performance corresponding to different failure modes are significant. Conclusion Structural stress method that is combined with shell element modeling significantly improves computational efficiency while ensuring analysis accuracy, and it is suitable for fatigue assessment and anti-fatigue design of large and complex welded structure.