Atom-by-atom engineering of nanomaterials requires atomic-level knowledge of the size evolution mechanism of nanoparticles, which remains one of the greatest mysteries in nanochemistry. Here we reveal atomic-level dynamics of size evolution reaction of molecular-like nanoparticles, i.e., nanoclusters (NCs) by delicate mass spectrometry (MS) analyses. The model size-conversion reaction is [Au23(SR)16]- → [Au25(SR)18]- (SR = thiolate ligand). We demonstrate that such isoelectronic (valence electron count is 8 in both NCs) size-conversion occurs by a surface-motif-exchange-induced symmetry-breaking core structure transformation mechanism, surfacing as a definitive reaction of [Au23(SR)16]- + 2 [Au2(SR)3]- → [Au25(SR)18]- + 2 [Au(SR)2]-. The detailed tandem MS analyses further suggest the bond susceptibility hierarchies in feed and final Au NCs, shedding mechanistic light on cluster reaction dynamics at atomic level. The MS-based mechanistic approach developed in this study also opens a complementary avenue to X-ray crystallography to reveal size evolution kinetics and dynamics.