Collision cross sections (CCSs) of ligand-protected metal clusters were evaluated using ion mobility mass spectrometry. The targets used in this study were phosphine-protected clusters [PdAu8(PPh3)8]2+ and [Au9(PPh3)8]3+, for which the total structures have been resolved by single-crystal X-ray analysis. The arrival time distributions of [PdAu8(PPh3)8]2+ as a function of the He flow rate in a cell located just in front of a traveling wave ion mobility cell filled with N2 buffer gas demonstrated that it got converted to another structural isomer having a smaller CCS, with the increase in the nominal collision energy. A similar phenomenon was observed for [Au9(PPh3)8]3+. These results were explained by the collisional excitation and cooling with the buffer gas inducing the conversion of the packing arrangement of the ligands rather than the atomic structure of the metallic core: the ligand layer was converted from disordered to the closely packed arrangement found in a single crystal during this process. This study showed that the ligand layer with a disordered arrangement in solution was retained during desolvation upon electrospray ionization and was annealed into the most stable closely packed arrangement by collisions. © 2018 American Chemical Society.