Currently, silicon vacancy (VSi) color centers in SiC are of significant interest due to their potential applications in quantum sensing and quantum communication. Meanwhile, femtosecond lasers, as a non-thermal processing technique, offer considerable advantages in machining hard and brittle materials, such as SiC. Femtosecond laser processing effectively increases the yield of VSi color centers in bulk materials and forms crater-shaped enriched regions on the surface. However, a notable gap exists in simulation methods to explain the mechanisms behind laser-assisted VSi color center generation. In this work, we develop a three-dimensional molecular dynamics (3D-MD) model using an integral hemi-ellipsoidal shell mathematical framework to simulate the interaction of Gaussian laser beams with bulk materials. Additionally, we calculate the transmittance, absorption coefficient, refractive index, and reflectivity of 4H-SiC. Subsequently, the absorption ratio of a 1030 nm laser in 350 μm thick 4H-SiC material is determined to simulate the energy loss during actual processing. Finally, the study analyzes the movement trajectories of VSi color centers and elucidates the source of VSi on the surface. This analysis explains the enrichment of color centers in the crater-shaped regions formed after laser deposition. Our work presents an effective 3D-MD modeling approach to study the processing mechanisms of laser interaction with semiconductor materials, offering insights into efficient VSi color center creation processes.