AbstractInvestigating the macro‐mechanical properties of polymer composites at the nanoscale is a challenging topic. Here we report the compressive performances of carbon fiber‐reinforced epoxy composites using molecular dynamics (MD) simulations. The evolution of microstructure and microscopic energy, including free volume, radius of gyration, dihedral angle, potential energy, and interaction energy, has been investigated to characterize compressive behaviors at the nanoscale. Molecular chains gradually bend, and the movement space of the molecular chains decreases during compression loading. The radius of gyration and dihedral angle are deformed into a state of irreversible plasticity to accommodate the microstructural transformation. The interaction energy increases and subsequently declines as the carbon fiber/epoxy interface gets closer, reflecting the transition of the internal structure. The inhomogeneity and interfacial concentration distribution of stress, and local molecular stiffness under various strains have been obtained to reveal the nanoscopic mechanism of epoxy failure and interface delamination during compression. This study reveals the compression behaviors and deformation mechanism of carbon fiber‐reinforced epoxy composites at the molecular level, providing directions and possibilities for molecular design and structural optimization of composites.Highlights The nanoscopic compression deformation of CFRP composites is studied. Microstructural evolution and conformation transformation are revealed. The evolution and transition of microscopic energy are analyzed. Micro‐mechanism of epoxy deformation and interface delamination is elucidated.