Nanosized particles can demonstrate dramatic performance in comparison to bulk materials in heterogeneous catalysis, due to their high density of under coordinate sites associated with altered electronic properties. The structural and compositional design of bimetallic nanoparticles can further afford the precise control of activity and selectivity via the geometric and electronic effects of secondary metals. Intermetallic compounds are one of the special alloys with defined stoichiometry and ordered crystal structure, which exemplifies them as ideal model catalysts for structure-property studies in catalysis. Direct colloidal synthesis of intermetallic nanoparticles requires the presence of organic capping agents, which limits the thermal stability of nanoparticles and complicates their surface structures. Mesoporous silica shells can be used to encapsulate monometallic and bimetallic nanoparticles with high sinter-resistance for high-temperature treatment, and enables their applications for harsh reaction conditions and fundamental mechanism studies. Several examples of silica-encapsulated nanoparticles have been demonstrated in this thesis to study their catalytic properties.