Chemoselective hydrogenation of CC and CO bonds in the cinnamaldehyde (CMA), was successfully performed with highly dispersed transition metal silicides-embedded in the porous carbon matrix (M2Si@C (M = Fe, Co, Ni)) nanocatalysts with a particle size of 8–12 nm, which were synthesized by a facile approach via microwave-assisted chemical vapor deposition (MWCVD) using organosilane and metal-organic-framework (MOFs-74)-templated porous carbon matrix-encapsulated transition metal (M@C) precursors. Compared with M@C, the activity of M2Si@C (M = Fe, Co, Ni) nanocatalysts obviously increases, which can be attributed that the overlayered carbon on metals has been destroyed during MWCVD processing, leading to the exposure of more active sites of catalysts. Due to the inherent electronic properties of metallic active sites in the metal silicides, the catalytic activity of Ni2Si@C was much higher than that of Co2Si@C and Fe2Si@C in the chemoselective hydrogenation of CMA. At total conversion of CMA, the Co2Si@C nanocatalyst was chemoselective for the hydrogenation of polar CO bonds (selectivity to cinnamyl alcohol of ∼60%), whereas Ni2Si@C nanocatalyst was highly chemoselective for the hydrogenation of non-polar CC bonds (selectivity to hydrocinnamaldehyde of ∼90%). The doping of silicon atoms with more electropositive into metals lattices in the M-Si intermetallic compounds (IMCs) influenced the adsorption of substrate molecule on the catalyst surface, slightly leading to the different reaction routes. In addition, the Co2Si@C and Ni2Si@C respectively maintain the robust stability in the hydrogenation of CMA. This result provided guidance on the design of catalyst via tuning the polarization properties of the inter-atoms in the IMCs according to the target product.