In the surface treatment of colloidal nanocrystals (NCs), S²⁻ ions have been widely employed as metal-free atomic ligands to efficiently replace the original long hydrocarbon ligands. Prior studies exclusively show that S²⁻ ions considerably quench the photoluminescence (PL) of semiconductor NCs (e.g., CdSe and PbS) during ligand exchange. Here we report that the influence of S²⁻ treatment on the luminescent properties of CdSe NCs is highly dependent on the NC size. We observe an unexpected PL brightening phenomenon when small CdSe NCs (<4 nm) are subject to S²⁻ treatment followed by incubation in the presence of air and light irradiation, whereas PL enhancement is not observed in large CdSe NCs (>4 nm) treated under the same conditions. Systematic characterization establishes the evolution of CdSe/CdS core–shell structures in small CdSe NCs arising from anion exchange between Se²⁻ and S²⁻, which in conjunction with the subsequent incubation process accounts for the PL enhancement. Notably, 2.1 nm CdSe NCs treated with (NH₄)₂S exhibit a PL quantum yield (QY) as high as ∼40% after 2 days of incubation, which is comparable to that of conventional hydrophobic CdSe/CdS core–shell NCs synthesized at high temperatures. Our studies demonstrate that S²⁻ ions can substantially substitute Se²⁻ in small CdSe NCs in addition to replacing the surface-coating ligands, enabling highly luminescent, hydrophilic CdSe/CdS core–shell NCs at room temperature.