Residual stresses change the stress ratio of fluctuating stresses, hence seriously affect the fatigue life of orthotropic steel decks (OSDs) under traffic loading. Residual stress distributions near the U rib-diaphragm joints are very complicated and need to be investigated further. In this paper, a systematic method has been proposed for calculating the residual stress field in the joint of U rib and diaphragm due to thermal cutting and welding. Firstly, a mathematical model of cutting heat sources was established to predict the temperature field. Then, a numerical elastoplastic thermomechanical model was built to predict the residual stress evolutions in a diaphragm-rib joint through the whole fabrication process involving flame cutting and welding. Moreover, the simulated temperature contours at the fusion zone and the residual stress distributions in the rib-diaphragm joint were compared and verified against the experimental ones. The numerical results showed a great agreement with the experimental ones, indicating that the heat source model can be used to accurately predict the temperature field during flame cutting. Finally, the validated numerical model was utilized to conduct parametrical analyses on the effects of thermal processing rates, e.g., the cutting and welding speeds and on the residual stress distribution in the rib-diaphragm joint. The results indicate that a faster cutting speed and a slower welding speed can decrease the residual stress magnitude at the rib-diaphragm joints and reduce the high-stress zone near the diaphragm cutouts.