Organic–inorganic hybrid heterogeneous nanocatalysts were successfully fabricated via covalent anchoring of cobalt(II) or copper(II) acetylacetonate complexes ([Co(acac)2] or [Cu(acac)2]) onto core–shell structured Fe3O4@SiO2 previously functionalized with 3-aminopropyltriethoxysilane (APTES). Surface functionalized nanomaterials were analyzed by a series of characterization techniques such as SEM, TEM, XRD, FT-IR, XPS, ICP-AES and VSM. The catalytic performance of the prepared nanocatalysts was evaluated in the epoxidation of styrene using eco-friendly air as the oxygen source. Both of the nanocomposites Fe3O4@SiO2–NH2–Co and Fe3O4@SiO2–NH2–Cu presented excellent styrene conversion (90.8% vs. 86.7%) and good epoxide selectivity (63.7% vs. 51.4%), much higher than the corresponding homogeneous counterparts. In addition, the magnetically recoverable nanocatalysts (MRNCs) can be conveniently separated and recovered from the reaction system by applying an external magnetic field and reused for four cycles with insignificant loss of catalytic activity. These results demonstrate that the heterogeneous nanocatalysts possess potential applications for green and sustainable development.