The stabilities of [M 12 Ag 32 (SR) 30 ] 4− (M=Ag, Au and SR=SPhF 2 , SPhCF 3 , SPhF) clusters having the same structure but different surface ligands or counter cations were systematically studied. It was clearly revealed that a subtle structural change in the surface ligands or counter cations could significantly alter the overall stability of [M 12 Ag 32 (SR) 30 ] 4− although they all had an electronic structure of 18-electron superatom shell closure. SPhF 2 was found as a better surface ligand than SPhCF 3 or SPhF to stabilize [M 12 Ag 32 (SR) 30 ] 4− . And the use of more bulky [(PPh 3 ) 2 N] + as the counter cations was revealed to be more deleterious to the overall stability of [M 12 Ag 32 (SR) 30 ] 4− clusters than PPh 4 + . [Au 12 Ag 32 (SR) 30 ] 4− was much more stable than [Ag 44 (SR) 30 ] 4− with the same surface ligands and counter cations. An exceptional stability was observed on (PPh 4 ) 4 [Au 12 Ag 32 (SPhF 2 ) 30 ] which was stable in DMF for more than 8 days in air at 80°C. More research efforts are still needed to deeply understand why a small structural change could result in a significant change in the stability of noble metal nanoclusters.