Layered core-shell structured Fungus hyphae (FH)/Fe3O4/graphene oxide (GO) nanocomposite spheres (FFGS) were successfully prepared by successively culturing FH in Fe3O4 or GO containing mediums. This strategy was low-cost, eco-friendly and easy to scale up for the preparation of core-shell structured FH mediated materials. Batch adsorption results showed that the core-shell structured FFGS was much better in the adsorption of methyl violet (MV) and uranium (U (VI)) than FH, FH/GO, and FH/Fe3O4, which might be attributed to its lower zeta potential. Specifically, the maximum adsorption capacity of FFGS was calculated to be 117.35 and 219.71 mg/g for MV (pH 7.0) at 303 K, and U (VI) (pH 5.0) at 293 K, respectively. According to the adsorption kinetics and adsorption isotherms, the mechanism of U (VI) adsorption on FFGS was dependent on the chemical adsorption, while MV was mainly physical adsorption. Furthermore, attributed to its magnetic shell, the FFGS could easily realize controllable magnetic separation. Thus, core-shell structured FFGS would be a promising adsorbent for the removal and recovery of MV or U (VI) from waste water.