Indentation experiments on differently oriented faces of monocrystalline copper were conducted to investigate the micro-deformation process at temperatures ranging from room temperature to 150 K. The morphologies and textures of the residual imprints were observed using electron microscopy. Distinct slip bands were observed inside the imprints at 150 K compared to smooth surfaces at room temperature. Molecular dynamics simulations were performed to identify the deformation process beneath the indentation region. The results showed that plastic deformation was inhibited with decreasing temperature, but elastic recovery during the unloading process was enhanced, resulting in inner slip bands (ISBs) being observable in the residual imprints. The performances of these ISBs were strongly associated with the angles between the indentation direction and major slip surfaces and could be considered microscopic forms on the surfaces of aggregated geometrically necessary dislocations (GNDs). This work helped reveal the micro-deformation mechanism of indentations inside imprints.