A ligand exchange strategy has been employed to understand the role of ligands on the structural and optical properties of atomically precise 29 atom silver nanoclusters (NCs). By ligand optimization, ∼44-fold quantum yield (QY) enhancement of Ag29(BDT)12-x(DHLA)x NCs (x = 1-6) was achieved, where BDT and DHLA refer to 1,3-benzene-dithiol and dihydrolipoic acid, respectively. High-resolution mass spectrometry was used to monitor ligand exchange, and structures of the different NCs were obtained through density functional theory (DFT). The DFT results from Ag29(BDT)11(DHLA) NCs were further experimentally verified through collisional cross-section (CCS) analysis using ion mobility mass spectrometry (IM MS). An excellent match in predicted CCS values and optical properties with the respective experimental data led to a likely structure of Ag29(DHLA)12 NCs consisting of an icosahedral core with an Ag16S24 shell. Combining the experimental observation with DFT structural analysis of a series of atomically precise NCs, Ag29-yAuy(BDT)12-x(DHLA)x (where y, x = 0,0; 0,1; 0,12 and 1,12; respectively), it was found that while the metal core is responsible for the origin of photoluminescence (PL), ligands play vital roles in determining their resultant PLQY.