Selective semi-hydrogenation of phenylacetylene to styrene is a crucial step in the polystyrene industry. Although Pd-based catalysts are widely used in this reaction due to their excellent hydrogenation activity, the selectivity for styrene remains a great challenge. Herein, we designed a mesoporous silica stabilized Pd-Ru@ZIF-8 (MS Pd-Ru@ZIF-8) nanoreactor with novel Pd and Ru single site synergistic catalytical system for semi-hydrogenation of phenylacetylene. The nanoreactor exhibited a superior performance, achieving 98% conversion of phenylacetylene and 96% selectivity to styrene. Turnover frequency (TOF) of nanoreactor was up to as high as 2,188 h⁻¹, which was 25 times and 5 times more than the single metal species catalysts, mesoporous silica stabilized Pd@ZIF-8 nanoreactor (MS Pd@ZIF-8), and mesoporous silica stabilized Ru@ZIF-8 nanoreactor (MS Ru@ZIF-8). This catalytic activity was attributed to the synergistic effect of Pd and Ru single site anchored strongly into the framework of ZIF-8, which reduced the desorption energy of styrene and increased the hydrogenation energy barrier of styrene. Importantly, since the ordered mesoporous silica was introduced into the nanoreactor shell to stabilize ZIF-8, MS Pd-Ru@ZIF-8 showed excellent reusability and stability. After the five cycles, the catalytical activity and selectivity still remained. This work provides insights for a synergistic catalytic system based on single-site active sites for selective hydrogenation reactions.