Understanding the origin of the photoluminescence (PL) phenomenon in ligand-protected metal nanoclusters is of paramount importance in both fundamental science and practical applications. In this study, we have studied the origin of fluorescence emission of two thiolate-ligand-protected Au 28 clusters (Au 28 (CHT) 20 and Au 28 (TBBT) 20 ) by means of density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations. Theoretical calculation results show that the ligand shell isomerization induces different ligand motif-to-metal core charge transfers (LMCT) of Au 28 (TBBT) 20 and Au 28 (CHT) 20 . Moreover, in Au 28 (CHT) 20 , the emission process of S 2 → S 0 can compete favorably with the internal conversion of S 2 → S 1 . Furthermore, the high quantum yield of Au 28 (CHT) 20 is attributed to its high symmetric structure, which leads to less energy dissipation during the structural relaxation process.