Highly stable and magnetically separable mesoporous silica nanospheres (MSNs) embedded with 4.6 ± 0.8 nm FeCo/graphitic carbon shell nanocrystals (FeCo/GC NCs@MSNs) were synthesized by thermal decomposition of metal precursors in MSNs and subsequent methane CVD. The FeCo/GC NCs@MSNs had a high specific surface area (442 m² g⁻¹), large pore volume (0.65 cm³ g⁻¹), and tunable size (65 nm, 130 nm, and 270 nm). Despite the low magnetic metal content (8.35 wt%), the FeCo/GC NCs@MSNs had a sufficiently high saturation magnetization (17.1 emu g⁻¹). This is due to the superior magnetic properties of the FeCo/GC NCs, which also enable fast magnetic separation of the nanospheres. The graphitic carbon shell on the FeCo NCs not only protects the alloy core against oxidation and acid etching in 35% HCl_(aq), but also facilitates non-covalent, hydrophobic interactions with the hydrocarbon chains of organic dyes such as methyl orange and methylene blue. Surface functionalization of the FeCo/GC NCs@MSNs with thiol groups provides efficient capacity for binding with Hg²⁺ ions. We have shown that the thiol-functionalized FeCo/GC NCs@MSNs (FeCo/GC NCs@MSNs-SH) work as multifunctional adsorbents for organic dyes (target organic pollutants) and Hg²⁺ ions (target inorganic pollutant). We also demonstrated that the FeCo/GC NCs@MSNs-SH are excellent recyclable adsorbents for methyl orange.