We investigate the electronic coupling between copper hexadecafluoro-phthalocyanine (F16CuPc) and epitaxial graphene (EG) on 6H-SiC (0001) using a combined approach of low-temperature scanning tunneling spectroscopy and electronic structure calculations. The molecules are preferentially adsorbed on monolayer EG than bilayer EG. Competing molecule-surface and intermolecular van der Waals interactions result in two well-ordered incommensurate phases. We show that the amount of charge transfer from EG to F16CuPc can be tuned by applied voltage or the thickness of graphene layers. A characteristic feature at similar to 0.4 eV above the Dirac point is identified in bilayer EG, which indicates its electronic structure is modified via introducing extra unoccupied states upon adsorption.