Topological insulators (TIs) are expected to realize new spintronic devices with low dissipative electrical transport. Organic molecule/TI interfaces have been investigated to explore the potential of multifunctional organic molecules for TI devices. However, there is no unified understanding of the interfacial electronic structure. The electronic structure of the molecular side must be examined to fully understand the phenomena at the interface. Thus, this paper reports the investigation of the interface between the electron‐donating organic molecule tetrathianaphthacene (TTN) and prototypical TI Bi2Se3 by ultraviolet photoemission spectroscopy (UPS), X‐ray photoemission spectroscopy (XPS), and angle‐resolved photoemission spectroscopy (ARPES). The deformation of the Fermi surface of the topological surface states as well as the formation of a 2D electron gas state (2DEG) at the interface occurs upon TTN deposition onto Bi2Se3. Confinement of the 2DEG into the surface arises from band‐bending accompanied by electron donation from TTNs to Bi2Se3 according to XPS and UPS. The knowledge obtained in this work shed new light on the understanding of the electronic structure of organic molecules/TI interfaces and open the door to the TI applications via modification by electronic functional organic molecules.