Highly Oriented Pyrolytic Graphite (HOPG) was half covered using aluminum foil and exposed to irradiation with 70 keV C+ ions at room temperature (~ 25 ℃). The surface layer (height = 178.3 ± 4.7 nm) of the irradiated area was destroyed, many nano-sized dendritic protrusions were observed and smooth inner layer was exposed. The peak area ratio (ID/IG) in Raman spectra increased after ion irradiation, indicating that a change in atomic structure and transformation from the sp2 to sp3 phase. The mechanical properties were explored using atomic force microscopy in peakforce mode, which revealed that the Young’s modulus of the exposed inner layer was similar to unirradiated area, while the Young’s modulus of the dendritic protrusions was higher. There findings provided further understanding of the HOPG at nanoscale, which is of value for practical implementation in related fields.