Charge transfer interaction at the gold (Au)/copper phthalocyanine (CuPc) interface, with Au on CuPc film, was investigated using vibrational techniques - Fourier Transform Infra Red and Raman spectroscopy, in combination with X- ray photoelectron spectroscopy. The charge transfer direction at this interface was found to be changing after annealing of the CuPc film, as compared to that before annealing. Molecule to metal charge transfer at the Au/CuPc interface observed for the as deposited film was found to be reversing to metal to molecule charge transfer for the annealed film. This reversal of charge transfer direction in the latter was attributed to the modified electronic structure/work function of the CuPc film and the varying orientation of CuPc molecules at the interface, brought about by the increased surface roughness, change in morphology, etc. The reversal in charge transfer direction was suggested to be supporting the reduction in parasitic contact resistance at the Au/CuPc interface for a top contact OFET with the annealed CuPc film, as compared to that with the as deposited film. This study demonstrates the influence of morphology of the organic semiconductor film on the charge transfer behaviour at the metal/organic semiconductor interface.