pH-sensitive photoluminescence (PL) is an important property of aqueous nanocrystals (NCs) towards NCs-based intelligent applications. Previous works mainly focused on the effect of pH during NC growth process on PL of the aqueous NCs. The effect of pH during application process on PL of as-prepared NCs is still not fully understood. In this work, we brought out a general mechanism for the pH-sensitive PL behaviors of as-prepared aqueous CdTe NCs capped by aqueous thiol ligands, such as carboxylic-acid-terminated 3-mercaptopropionic acid (MPA) and thioglycolic acid (TGA) ligands, hydroxyl-terminated 1-thioglycerol (TG) ligands and amine-terminated 2-mercaptoethylamine (MA) ligands. A major contribution of this work is finding the key role of ligand terminal groups in the diffuse process of free Cd-ligand complexes toward NCs. This terminal group effect is the main reason for PL alteration of NCs during pH adjustment process. Besides the terminal group effect, PL of aqueous NCs is also affected by the aggregation effect, the thiol group effect and the counter ion effect. These effects make different contributions to PL of NCs at different pH ranges. By using this mechanism, we successfully explained the complex pH-sensitive PL behaviors of MPA, TGA, TG and MA-capped CdTe NCs.