Controlling the type and density of charge carriers by doping is the key step for developing graphene electronics. However, direct doping of graphene is rather a challenge. Based on first-principles calculations, a concept of overcoming doping difficulty in graphene via substrate is reported.We find that doping could be strongly enhanced in epitaxial graphene grown on silicon carbide substrate. Compared to free-standing graphene, the formation energies of the dopants can decrease by as much as 8 eV. The type and density of the charge carriers of epitaxial graphene layer can be effectively manipulated by suitable dopants and surface passivation. More importantly, contrasting to the direct doping of graphene, the charge carriers in epitaxial graphene layer are weakly scattered by dopants due to the spatial separation between dopants and the conducting channel. Finally, we show that a similar idea can also be used to control magnetic properties, for example, induce a half-metallic state in the epitaxial graphene without magnetic impurity doping.