Highly oriented pyrolytic graphite is ablated by femtosecond laser in air and vacuum, respectively. The morphologies and material components of the ablated target surface are examined by scanning electron microscopy and micro-Raman spectroscopy. For laser fluence no less than 0.5 J/cm(2), the laser-induced periodic surface grooves formed in air are found to be much less clearer than those formed in vacuum; beneath the amorphous carbon debris, the surface ablated in air is composed of nanocrystalline graphite, but in vacuum it retains the ordered graphite structure. The thermal relaxation of the ablated target induced by air-assisted heat transfer is considered to be the main reason for the differences. The transportation of air molecules along the surface, the classical size effect of heat conduction and high solid-air heat transfer coefficient in nanoscale enhance the air-assisted heat transfer.