Although the restriction of intramolecular motion has been well recognized as the fundamental of aggregation induced emission enhancement (AIEE), the regulation mechanism of gold nanoclusters (AuNCs) based AIEE system are still unclear. In this paper, we have investigated the Zn2+-induced AIEE process of thiolate ligands (i.e., cysteine, glutathione and an 8-mer peptide) protected AuNCs, which shows a pH-dependent evolution from single AuNCs to spheric aggregates to irregular network. Using photoluminescent enhancement ratio as an index, the concept of “mid-pH” is proposed to indicate the optimal pH for the formation of spheric AuNCs aggregates. Importantly, the surface ligands allow the formation of spheric AuNCs aggregates at tunable mid-pH between 5.7 and 7.5. Owing to the appropriate size and surface peptide targetability, the spheric AuNCs aggregates can be successfully screened for targeted tumor cell uptake and imaging at physiological pH. The cell uptake mechanism study showed that AuNCs aggregates was specifically recognized by arginine-glycine-aspartic acid (RGD) sequence on the ligand and integrin αvβ3 on the cell surface, thus mainly through clathrin-mediated endocytosis. This work provides new sight to artificially regulate the construction of efficient cellular imaging probes.