The irreversible capacity loss of the carbon electrode in lithium-ion batteries at the first cycle is caused mostly by surface film growth. We inspected an unknown irreversible capacity loss (UICL) of the natural graphite electrodes. The charge/discharge behavior of graphite and meso-phase carbon microbeads heat-treated at 2800 degrees C (MCMB28) as the materials of the carbon anode in the lithium-ion battery were compared. It was found that the capacity loss of the natural graphite electrode in the first cycle is caused not only by surface film growth, but also by irreversible lithium-ion intercalation on the new formed surface at the potential range of lithium intercalation, while the capacity loss of the MCMB28 electrode is mainly originated from surface film growth. The reason for the difference of their irreversible capacity losses of these two kinds of carbon material was explained in relation to their structural characteristics.