||Topological insulators (TIs) have gained considerable attention owing to their topologically protected helical edge states called topological surface states. To employ TIs, it is necessary to reduce film thickness and suppress effects from the bulk carrier. When the film thickness is less than 5 quintuple layers (QLs), the top and bottom surface states overlap, thereby increasing surface bandgap. In this study, we investigate the suppression of the hybridization of surface states in a 3-QL Bi2Se3/graphene heterostructure. In the 3-QL Bi2Se3 film grown on graphene, surface states affected by strain, and band bending effects from graphene are localized to the top and bottom and possess a closed bandgap. Further, we investigated transport properties in the 3-QL Bi2Se3/graphene heterostructure and verified the independent transport channels of Bi2Se3 and graphene, and the long coherence length of 534 nm. In conclusion, the closed bandgap and long coherence length in the 3-QL Bi2Se3/graphene heterostructure implies that the proximity effect in a TI/non-TI heterostructure can be attractive for future applications, beyond the physical and topological thickness limit.