Accumulated heat input during layer deposition causes high residual stress in the Wire-Arc Additive Manufacturing (WAAM) components. The developed residual stress results in defects like distortion, delamination, cracks, and low fatigue life. To deal with such engineering problems, numerical methods have always been required. It gives an insight into the system that can be used for real-world applications. Consequently, a sequentially coupled finite element model has been developed to simulate the thermal–structural behavior of the feedstock during and after deposition in the WAAM process. Precisely, a novel multi-level layer-wise heat input approach characterized by four different stages is compared with the layer-wise single heat input strategy. The variation of thermal and residual stress distributions has been studied based on the different cases proposed related to layer-wise multi-level heat loading. A good agreement between predicted and experimentally observed temperature and residual stress values has been observed. The developed framework predicted thermal distribution with an average error of 9.71%, 9.13%, 7.57%, and 4.52% for case #1, case #2, case #3, and case #4, respectively. In addition to that, longitudinal stresses in the modeled component recorded a reduction of 17.94% for four-level heat input (case #4) compared to the respective value observed in case #1. Therefore, a multi-level heat input strategy is recommended over a single-level heat input approach for the components with small deposition lengths manufactured through the WAAM process.