Collision-induced dissociation (CID) patterns of the phosphine-protected Au-based clusters [PdAu8(PPh3)8]2+ (PdAu8) and [Au9(PPh3)8]3+ (Au9), featuring crown-shaped M@Au8 (M = Pd, Au) cores, were investigated. For PdAu8, ordinary sequential PPh3 losses (PdAu8 → [PdAu8(PPh3)m]2+ + (8 - m)PPh3 (m = 7, 6, 5)) were observed. In contrast, Au9 underwent cluster-core fission (Au9 → [Au6(PPh3)6]2+ (Au6) + [Au3(PPh3)2]+ (Au3)) upon sufficiently high energy collision, associated with splitting the number of valence electrons in the superatomic orbitals from 6e (Au9) into 4e (Au6) and 2e (Au3). Density functional theory calculations revealed oblate and prolate cores of Au9 and Au6 with semiclosed superatomic electron configurations of (1S)2(1Px)2(1Py)2 and (1S)2(1Pz)2, respectively. This result indicated a significant deformation of the cluster-core motif during the CID process. We attribute the clear difference between PdAu8 and Au9 to the softer Au-Au bond in Au9 and propose that the collision-induced structural deformation plays a critical role in the fission.