This study presents the first atomistic modeling investigation of Additive Friction Stir Deposition (AFSD), providing detailed insights into thermomechanical and microstructural evolution at the nanoscale. Molecular dynamics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) were employed to capture the complex interplay of rotation, translation, and frictional heating during aluminum deposition. The aluminum system was modeled using an Embedded Atom Method potential with periodic boundary conditions, enabling realistic representation of material flow and layer formation. Comprehensive atomistic diagnostics revealed that severe plastic deformation is highly localized at the tool-substrate interface, with elevated shear strain concentrated beneath the rotating feedstock. Analysis of atomic coordination numbers demonstrated significant lattice distortion in the interfacial region, while dislocation structure characterization identified defect clustering associated with plastic strain accumulation. Voronoi tessellation-based analyses quantified heterogeneous atomic packing, free-volume generation, and cavity formation, correlating spatially with regions of intense deformation. These results show that AFSD promotes metallurgical bonding through confined interfacial mixing while preserving substrate integrity. The atomistic framework developed here establishes a foundation for understanding deformation mechanisms, optimizing process parameters, and predicting microstructural evolution in solid-state additive manufacturing, offering insights complementary to experimental observations at macroscopic scales.