The electronic and atomic structures of topological insulator Bi2Se3, upon Ag atom deposition, have been investigated by combined experimental methods of scanning tunneling microscopy (STM), photoelectron spectroscopy, and first-principles calculations. We show from the results of STM that the deposited Ag atoms are stabilized beneath the surface instead of being adsorbed on the topmost surface. We further reveal from the angle-resolved photoemission spectroscopy that the Bi₂Se₃(0001) topological surface states stay uninterrupted after a large amount of absorption of Ag atoms. Our analysis of the photoelectron intensity of Ag core states excited by soft X-ray suggests that a large amount of deposited Ag atoms diffused into a deeper place, which is beyond the probing depth of X-ray photoelectron spectroscopy. The first-principles calculations identify the octahedral site in the van der Waals gaps between quintuple layers to be the most favorable locations of Ag atoms beneath the surface, which yields good agreement between the simulated and experimental STM images. These findings pave an efficient way to tailor the local lattice structures of topological insulators without disturbing the topologically nontrivial surface states.