Modification of epitaxial graphene on silicon carbide (EG/SiC) was explored by ion implantation using 10 keV nitrogen ions. Fragments of monolayer graphene along with nanostructures were observed following nitrogen ion implantation. At the initial fluence, sp3 defects appeared in EG; higher fluences resulted in vacancy defects as well as in an increased defect density. The increased fluence created a decrease in the intensity of the prominent peak of SiC as well as of the overall relative Raman intensity. The X-ray photoelectron spectroscopy (XPS) showed a reduction of the peak intensity of graphitic carbon and silicon carbide as a result of ion implantation. The dopant concentration and level of defects could be controlled both in EG and SiC by the fluence. This provided an opportunity to explore EG/SiC as a platform using ion implantation to control defects, and to be applied for fabricating sensitive sensors and nanoelectronics devices with high performance.