Thermally induced residual stresses due to welding can significantly impair the performance and reliability of welded structures. From a structural integrity perspective of welded structures, it is necessary to have an accurate spatial and temporal thermal distribution in the welded structure before stress analysis is performed. Existing research has ignored the effect of fluid flow in the weld pool on the temperature field of the welded joint. Previous research has established that the weld pool depth/width (D/W) ratio and heat affected zone (HAZ) are significantly altered by the weld pool dynamics. Hence, for a more accurate estimation of the thermally induced stresses it is desired to incorporate the weld pool dynamics into the analysis. Moreover, the effects of microstructure evolution in the HAZ on the mechanical behavior of the structure need to be included in the analysis for better mechanical response prediction. In this study, a three-dimensional numerical model for the thermomechanical analysis of gas tungsten arc (GTA) welding of thin stainless steel butt-joint plates has been developed. The model incorporates the effects of thermal energy redistribution through weld pool dynamics into the structural behavior calculations. Through material modeling the effects of microstructure change/phase transformation are indirectly included in the model. The developed weld pool dynamics model includes the effects of current, arc length, and electrode angle on the heat flux and current density distributions. All the major weld pool driving forces are included, namely surface tension gradient induced convection, plasma induced drag force, electromagnetic force, and buoyancy. The weld D/W predictions are validated with experimental results. They agree well. The workpiece deformation and stress distributions are also highlighted. The mathematical framework developed here serves as a robust tool for better quantification of thermally induced stress evolution and distribution in a welded structure by coupling the different fields in a welding process.