We demonstrate the use of chemical-vapor-deposited (CVD) graphene as an effective indium-tin-oxide (ITO) electrode surface modifier to engineer the organic donor-acceptor heterojunction interface properties in an inverted organic solar cell device configuration. As revealed by in situ near-edge X-ray adsorption fine structure measurement, the organic donor-acceptor heterojunction, comprising copper-hexadecafluoro-phthalocyanine (F16CuPc) and copper phthalocyanine (CuPc), undergoes an obvious orientation transition from a standing configuration (molecular π-plane nearly perpendicular to the substrate surface) on the bare ITO electrode to a less standing configuration with the molecular π-plane stacking adopting a large projection along the direction perpendicular to the electrode surface on the CVD graphene-modified ITO electrode. Such templated less-standing configuration of the organic heterojunction could significantly enhance the efficiency of charge transport along the direction perpendicular to the electrode surface in the planar heterojunction-based devices. Compared with the typical standing organic-organic heterojunction on the bare ITO electrode, our in situ ultraviolet photoelectron spectroscopy experiments reveal that the heterojunction on the CVD graphene modified ITO electrode possesses better aligned energy levels with respective electrodes, hence facilitating effective charge collection.