The femtosecond laser ablation of metals is a complex and violent nonequilibrium process, and numerous studies have sought to reveal the evolution of a single physical phenomenon, such as laser-induced periodic surface micro-nanostructures or plasma eruptions. By considering the multiphysics scenarios of energy and heat transfer, structural mechanics, hydrodynamics, and nucleation dynamics, a femto-nanosecond and nano-micrometer multiscale framework combining electron–phonon-coupled heat transfer, lattice deformation, phase transition, and plasma eruption was constructed to describe the heat and mass transfer mechanism of femtosecond laser–copper interaction. A multiphysics model was proposed in this study to simulate the ablation process with different laser fluences. Ablation occurs at low near-threshold fluences primarily via a combination of the thermal phase transition process of melting and thermoplastic deformation coupled with the nonthermal phase transition process of hot electron explosion. Marangoni convection and non-uniform nucleation at the solid–liquid interface create micro-nano structures on the surface of the ablation crater. At a high laser fluence, plasma plumes are emitted via gasification and eruption, and as the material is heated to decrease its density, the surface is broken into a micro-column structure, and then the micro-columns fracture and erupt to form micro-nano structures and plasma plumes. Numerical results offer a better understanding of surface topography modifications and plasma plume evolution and promote the application of femtosecond laser precision fabrication in the fields of aviation, mechanics, electronics, and materials engineering.