Recent Van der Waals hetero-interfaces consist of two-dimensional (2D) materials, the organic molecules of which have been intensively studied to enable the enhancement of their excellent opto-electrical properties. For instance, if the organic molecules are properly designed, it enables manipulation of the electronic structure of 2D materials, as well as their energy level alignment. The type of energy level alignment, which generally can be classified as straddling type-I and staggered type-II, can significantly impact the optical behavior at the hetero-interfaces.In conventional materials, this energy level alignment can be predicted by the energy level difference between ionization energies, i.e.the rule of vacuum level alignment. However, this rule is sometimes no longer valid without the consideration of unique 2D properties stemming from theatomical thin thickness. Furthermore, the mechanism of the aforementioned electronic structure turning is not properly understood so far. In this contribution, first, we demonstrate the controlling of the electronic structure of 2D materials itself using the modelfunctional (acceptor for 2,3,5,6-Tetrafluoro-7,7,8,8-tetracyanoquinodimethane)and (donor for Dichloro[hexamethylbenzene] ruthenium[II] dimer] organic molecules. Those are evidenced by the measurement of the angle-resolved and X-ray photoelectron spectroscopy. In the same manner, the turning of energy level alignment between hetero-interfaces was also discussed. The impact of the surrounding environment i.e. the substrate effect on its control and their mechanism will be addressed. These results help not only to understand interfacial physical phenomena, but also helps design optimized opto-electrical applications.