Abstract Isomer-resolved multiphoton dissociation (PD) with 3.5 eV and collision-induced dissociation (CID) were applied to small carbon cluster cations, Cn+ (n = 7–10), to investigate correlations between the isomer structures and dissociation reactivities. Linear and cyclic isomers, which coexist in this size range, were separated by ion mobility spectrometry using a home-made drift cell. The linear isomers mainly produced C3-loss fragments, while cyclic ones showed C2-loss as well as C3-loss products. The C2-loss products were predominantly observed by PD, whereas comparable amounts of C2- and C3-loss products were observed by CID. The range of the excitation energy of CID was overlapped with that of PD, whereas the former range was wider than the latter. Plausible origins of the difference between the fragment distributions from the cyclic and linear isomers are discussed in terms of the energetics of the fragment ions.