Femtosecond laser ablation is widely applied in high-precision machining of microholes in aeroengine turbine blades. To further explore the mechanism of action during the laser processing of microholes, numerical simulations were performed on the basis of a molecular dynamics (MD) method coupled with a two-temperature model (TTM). Laser irradiation on the surface of copper for different femtosecond-laser processing parameters is investigated in this work. Through the femtosecond-laser single-pulse central ablation simulation model, the laser energy flux density in a Gaussian laser spot range was discretized and analyzed to calculate the ablation depth at multiple points separately. The cross-sectional morphology of the femtosecond-laser single-pulse ablation pits was approximated and fitted. Finally, a 3D simulation model of the whole process of multiscale femtosecond-laser spiral processing microholes was established by superimposing multipulse femtosecond-laser spiral trajectories. This provides a theoretical basis for analyzing the evolution of geometric parameters and morphological characteristics of the hole during machining with specific laser and process parameters.