Electronic structures of copper hexadecafluorophthalocyanine (F16CuPc)/graphene with different defect density were studied with ultra-violet photoelectron spectroscopy. We showed that the charge transfer interaction and charge flow direction can be interestingly tuned by controlling the defect density of graphene through time-controlled H2 plasma treatment. By increasing the treatment time of H2 plasma from 30 s to 5 min, both the interface surface dipole and the electron transporting barrier at F16CuPc/graphene interface are significantly reduced from 0.86 to 0.56 eV and 0.71 to 0.29 eV, respectively. These results suggested that graphene's defect control is a simple approach for tuning electronic properties of organic/graphene interfaces.