We report an indirect method for the effective replacement of ligands on the surface of Au nanocrystals with different morphologies. The method involves the deposition of an ultrathin layer of Ag to remove a strong capping agent such as cetyltrimethylammonium chloride (CTAC), followed by selective etching of the Ag layer in the presence of citrate ions as a stabilizer. Using multiple characterization techniques, we confirm that the surface of the Au nanocrystals is covered by citrate ions after the indirect ligand exchange process, and there is essentially no aggregation during the entire process. We also demonstrate that this method is effective in suppressing the toxicity of Au nanospheres by completely replacing the initially used CTAC with citrate.