Yolk-shell nanoparticles (YSNs) with active metal cores have shown promising applications in nanoreactors with excellent catalytic performance. In this work, Fe(0)@SiO2 YSNs were synthesized by a sequential "two-solvents" impregnation-reduction approach. Specifically, FeSO4 aqueous solution was introduced into the preformed hollow mesoporous silica spheres (HMSS), dispersed in n-hexane, via a "two-solvent" impregnation way. Subsequently, aqueous solution of sodium borohydride (NaBH4) was introduced into the cavity of HMSS by the same way, leading to the formation of Fe core inside the HMSS through the reaction between Fe(2+) and NaBH4. The resulting Fe(0)@SiO2 YSNs possess distinctive structures, including active cores, accessible mesoporous channels, protective shells, and hollow cavities. To present the catalytic performance of YSNs nanoreactors, Fenton-like catalytic oxidation of phenol was chosen as the model catalysis reaction. In addition to the Fe(0)@SiO2 YSNs, two other materials were also applied to the catalytic system for comparison, including Fe@SiO2 composites with iron nanoparticles sticking on the outer shells of HMSS (Fe@SiO2-DI) and bare iron nanoparticles without HMSS (bare Fe(0)), respectively. The catalytic results show that Fe(0)@SiO2 YSNs exhibit higher catalytic rate toward phenol removal at 2-fold and 4-fold as compared to that of Fe@SiO2-DI and bare Fe(0), indicating the outstanding catalytic property of YSNs nanoreactors. To further clarify the relationship between catalytic properties and structural characteristics, the adsorption experiments of the three samples were also performed in the absence of H2O2. Other than catalytic results, Fe(0)@SiO2 YSNs show slightly higher adsorption efficiency than the other two samples, indicating the accessibility of nanoreactors. This result demonstrates that the removal of phenol in the oxidation system of Fe(0)@SiO2 YSNs may have contributed to the structure-enhanced effect of YSNs as nanoreactors.