Molecule–substrate interaction plays a vital role in determining the electronic structures and charge transfer properties in organic-transition metal oxides (TMOs) hybridized devices. In this work, the interactions at the FePc/MoO₃ interface has been investigated in detail by using synchrotron radiation photoemission spectroscopy (SRPES) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Compared with the annealing of the bare MoO₃ film, the FePc adsorption is found to promote the thermal reduction of the underlying MoO₃ film. XPS and NEXAFS experimental results unanimously demonstrate a strong electronic coupling between FePc molecules and the MoO_x (x < 3) substrate. A direct Fe–O coordination at the interface as well as an electron transfer from the molecules toward the substrate is proposed. This strong coupling is compatible with a facile electron transfer from FePc molecules toward electrode through a MoO_x interlayer. The understanding of the molecule–substrate interaction at the atomic level is of significance in engineering functionalized surfaces with potential applications in nanoscience, molecular electronics and photonics.