The evolution of electronic structures and morphology of dinaphthothienothiophene (DNTT) thin films on highly oriented pyrolytic graphite, due to the incorporation of a polar chlorogallium phthalocyanine (ClGaPc) molecular layer at the interface, substitution of DNTT with alkyl side-chain incorporated S-shaped DNTT (S-DNTT-C10), and thermal annealing, were investigated using photoelectron spectroscopic techniques to check the possibility of proper energy level alignment at the metal-organic interface, which is one of the key challenges to improve the charge transport in organic semiconductor-based devices. A significant modulation in the vacuum level (VL) and a small downward shift in the highest occupied molecular orbital (HOMO) level with an intermediate charge injection level (CIL) are evident in the DNTT thin film due to the incorporation of the ClGaPc layer at the interface. This is a clear signature of the molecular dipole layer (of well-ordered Cl-up orientated ClGaPc molecules)-induced realignment of the molecular energy levels of the DNTT thin films. On the other hand, a noticeable downward shift in the VL, a signature of an improvement in the bulk coverage, is evident in the S-DNTT-C10 film, which can be attributed to the presence of aliphatic hydrocarbons in the alkyl side-chain incorporated molecule. Furthermore, a double-peak-like HOMO level is evident in the S-DNTT-C10 film, which can be attributed to the two distinct orientations/arrangements of the molecules, one at the interface and other in the remaining part of the film. The formation of an intermediate CIL, through incorporation of a molecular dipole layer at the interface, is helpful to overcome the large hole injection barrier, while the enhancement of molecular coverage at the metal-organic interface and thereafter, through molecular engineering, is useful to increase the hole injection area, both of which are of immense importance in improving the device performances.