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The existence of a gapless Dirac surface band of a three dimensional (3D) topological insulator (TI) is guaranteed by the nontrivial topological character of the bulk band, yet the surface band dispersion is mainly determined by the environment near the surface. In this Letter, through in situ angle-resolved photoemission spectroscopy and first-principles calculation on 3D TI-based van der Waals heterostructures, we demonstrate that one can engineer the surface band structures of 3D TIs by surface modifications without destroying their topological nontrivial property. The result provides an accessible method to independently control the surface and bulk electronic structures of 3D TIs, and sheds light on designing artificial topological materials for electronic and spintronic purposes.