The invention discloses a core-shell structure catalyst for fuel cells and its pulse electrodeposition preparation method. The active component of the catalyst is a nanoparticle with a core-shell structure, and an active metal is cladded in the form of an ultrathin shell on the surface of a carbon carrier loaded metal or alloy nanoparticle serving as a core. The catalyst takes a non-platinum noble metal or transition metal as the core, and adopts more than one of Pt, Ir or Au as the shell. The preparation method includes: preparation of the nanoparticle serving as the core, making of a working electrode for pulse electrodeposition, and preparation of the catalyst by pulse electrodeposition. The catalyst can be used as an anode or cathode catalyst of a low temperature fuel cell. The obtained catalyst has very high stability. Compared with underpotential deposition, the method is simple to operate, has no need for inert atmosphere protection, and is more suitable for large-scale industrial production, also can greatly reduce the noble metal consumption of fuel cells, and greatly reduce the cost of fuel cells, thus having great significance in promoting the commercialization process of fuel cells.