Isomer-resolved multiphoton dissociations (PDs) with 4.66-eV laser photons were applied to carbon and silicon cluster cations, C\hbox{$_{n}^{{+}}$}+n (n = 32, 34, 36, and 38) and Si\hbox{$_{m}^{{+}}$}+m (m = 24–27), in order to investigate correlations between the isomer structures and dissociation reactions. Cyclic and fullerene structures of C\hbox{$_{n}^{{+}}$}+n and prolate and spherical isomers of Si\hbox{$_{m}^{{+}}$}+m, which are the coexisting isomers in these size ranges, were separated by ion mobility spectrometry, followed by photolysis using a tandem reflectron mass spectrometer. Photofragment ion distributions were revealed to depend on the parent isomer structures. Dissociation mechanisms were discussed from the fragment ion distributions.