The electronic structures and core-level spectra of chlorogallium phthalocyanine (ClGaPc) molecules of different thicknesses (submonolayer to multilayer) adsorbed on a polycrystalline Au substrate and a highly oriented pyrolytic graphite (HOPG) substrate, before and after thermal annealing, were investigated using photoelectron spectroscopic techniques for better understanding the charge-transfer properties. The energy-level diagrams (ELDs) of the ClGaPc thin films are found to evolve with film thickness, substrate nature, and thermal annealing. The interfacial dipole moment in the active Au substrate and the molecular dipole moment in the inactive HOPG substrate mainly dictate the ELD. Annealed monolayer films on both the substrates seem to adopt a similar well-ordered Cl-up orientated molecular organization, which is quite interesting, as it certainly indicates a substrate-nature-independent energy minimum configuration. The strong interaction of the active Au substrate gives rise to additional charge transfer and state transfer (of Ga) as evident from the formation of a former lowest unoccupied molecular orbital (F-LUMO) level in the highest occupied molecular orbital (HOMO) region and a low binding energy peak in the Ga 2p3/2 core level. The presence of strong F-LUMO and molecular-dipole-related HOMOd levels in the predicted monolayer of well-ordered Cl-up oriented molecules on the Au and HOPG substrates, respectively, creates the optimum energy-level alignment (ELA) for both the systems, while the opposite shift of the vacuum levels in two different substrates makes the ionization potential (IP) for such a monolayer either minimum (on the Au substrate) or maximum (on the HOPG substrate), which is useful information for tuning the charge injection across the interface in organic semiconductor-based devices.