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.