The molecular orientation of organic semiconductors on a solid surface could be an indispensable factor to determine the electrical performance of organic-based devices. Despite its fundamental prominence, a clear description of the emergent two-dimensional layered material-organic interface is not fully understood yet. In this study, we reveal the molecular alignment and electronic structure of thermally deposited N,N'-dibutyl-3,4,9,10-perylene-dicarboximide (PTCDI-C4) molecules on natural molybdenum disulfide (MoS) using near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The average tilt angle determination reveals that the anisotropy in the π* symmetry transition of the carbon K-edge (284-288 eV range) is present at the sub-monolayer regime. Supported by ultraviolet photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS), and resonant photoemission spectroscopy (RPES) measurements, we find that our spectroscopic measurements indicate a weak charge transfer established at the PTCDI-C4/MoS interface. Sterical hindrance due to the C4 alkyl chain caused tilting of the molecular plane at the initial thin film deposition. Our result shows a tunable interfacial alignment of organic molecules on transition metal dichalcogenide surfaces effectively enhancing the electronic properties of hybrid organic-inorganic heterostructure devices.