Understanding the effect of intermolecular and molecule-substrate interactions on molecular electronic states is key to revealing the energy level alignment mechanism at organic-organic heterojunctions or organic-inorganic interfaces. In this paper, we investigate the energy level alignment mechanism in weakly interacting donor-acceptor binary molecular superstructures, comprising copper hexadecafluorophthalocyanine (F16CuPc) intermixed with copper phthalocyanine (CuPc), or manganese phthalocynine (MnPc) on graphite. The molecular electronic structures have been systematically studied by in situ ultraviolet photoelectron spectroscopy (UPS) and low-temperature scanning tunneling microscopy/spectroscopy (LT-STM/STS) experiments and corroborated by density functional theory (DFT) calculations. As demonstrated by the UPS and LT-STM/STS measurements, the observed unusual energy level realignment (i.e., a large downward shift in donor HOMO level and a corresponding small upward shift in acceptor HOMO level) in the CuPc-F16CuPc binary superstructures originates from the balance between intermolecular and molecule-substrate interactions. The enhanced intermolecular interactions through the hydrogen bonding between neighboring CuPc and F16CuPc can stabilize the binary superstructures and modify the local molecular electronic states. The obvious molecular energy level shift was explained by gap-state-mediated interfacial charge transfer.