To apply graphene to the semiconductor device, it is important to dope molecules and metals on graphene because the carrier density of the graphene layer can be controlled by doping metals and molecules. Here, we introduced the nitrogen ions to modify the graphene surface and investigated its surface property changes. Graphene layer grown on 6H-SiC(0001) were irradiated with the nitrogen ion energy of 50, 100, and 150 eV, respectively. Surface property changes were studied using photoemission spectroscopy (PES), near edge X-ray adsorption spectroscopy (NEXAFS) and atomic force microscopy (AFM). N 1s core-level spectra and N K-edge show three kinds of nitrogen species; nitrogen gas, graphite-like and pyridine-like nitrogen. And their relative intensities show the ion energy dependency. Also, the measured work function changes verified that increased nitrogen ions on graphene showed n-type doping characteristics.