Bridging the structure-properties relationship of bimetallic catalysts is essential for the rational design of heterogeneous catalysts. Different from random alloys, intermetallic compounds (IMCs) present atomically-ordered structures, which is advantageous for catalytic mechanism studies. We used Pt-based intermetallic nanoparticles (iNPs), individually encapsulated in mesoporous silica shells, as catalysts for the hydrogenation of nitroarenes to functionalized anilines. With the capping-free nature and ordered atomic structure, PtSn iNPs show >99% selectivity to hydrogenate the nitro group of 3-nitrostyrene albeit with a lower activity, in contrast to Pt3Sn iNPs and Pt NPs. The geometric structure of PtSn iNPs in eliminating Pt threefold sites hampers the adsorption/dissociation of molecular H2 and leads to a non-Horiuti-Polanyi hydrogenation pathway, while Pt3Sn and Pt surfaces are saturated by atomic H. Calculations using density functional theory (DFT) suggest a preferential adsorption of the nitro group on the intermetallic PtSn surface contributing to its high selectivity.