Effects of surface chemistry on energy levels or optical properties of semiconductor nanocrystals have attracted considerable attention and show great promise in broad applications. Yet, it remains challenging to controllably tune the photoluminescence (PL) of quantum dots (QDs) by manipulating surface ligands. Herein, we investigated effects of the ligand, glutathione (GSH), on PL properties of near-infrared (NIR) Ag₂Se QDs by “on-surface” manipulation, that is, precisely manipulating the chelating group without dissociating the ligand from the surface. The anchoring of the amino group was found to be controlled by solution pH, whereas the binding of the thiol group to the Ag⁺ was pH independent, maintaining the “on-surface” state of GSH. By tuning the pH-controlled binding of amino groups, the energy level or the bandgap of Ag₂Se QDs could be increased by up to 140 meV. The increased bandgap resulted in the blueshift of PL spectrum, which could be reversibly tuned by up to 75 nm. The pH-mediated tunable PL properties of QDs could also be extended to other nitrogen-containing pH-sensitive groups which could coordinate to the Ag⁺, not limited to the amino group. Our work would facilitate the study of nanocrystal surface chemistry and our model that the binding of amino groups affected energy levels of Ag₂Se QDs might facilitate new insights into the electronic structure and energy level of other QD-ligand complexes.