In this paper, multi-layer and multi-pass arc additive manufacturing experiments were carried out on the Q345 substrate using Y309L welding wire. Based on MSC. Marc software, a thermal-elastic-plastic finite element method was developed to numerically simulate the temperature field, stress field, and deformation during the additive manufacturing process. The effects of the substrate thickness and interpass temperature on the temperature field, stress field, and deformation were discussed. The results indicated that the deposition materials at different positions experienced different thermal cycles, which might lead to the non-uniform microstructure and mechanical properties within the workpiece. The interpass temperature and the thickness of the substrate influenced the residual stress distribution in the additive manufactured structure. A low interpass temperature and thin substrate was able to effectively reduce the tensile residual stress. The thick substrate resulted in a small angular deformation of the substrate during the additive manufacturing process.