Megranate-like nanoparticles possess a unique structure that is composed of multiple cores and shells, which is different from simple yolk-shell nanoparticles. Megranate-like nanoparticles can combine the properties of each component and be used as nanoreactors. This study describes the preparation of bifunctional megranate-like nanoreactors, consisting of multiple metal cores and thiol modified mesoporous SiO2 shells. Different metal nanoparticles (Pd, Pt, Au) can be incorporated into the structure as cores, and the thiol group in the shells can be oxidized to acidic -SO3H. The megranate-like nanoparticles show good bifunctional catalytic properties and recyclability in a cascade catalytic reaction for the desired benzimidazole derivative. Moreover, the individual components of the megranate-like nanoparticles also show good catalytic activities in the hydrogenation reduction of nitro-aromatics and the deprotection reaction of benzaldehyde dimethyl acetal.