Three-component microspheres containing an SiO2-coated Fe3O4 magnetite core and a layered double hydroxide (LDH) nanoplatelet shell have been synthesized via an in situ growth method. The resulting Fe3O4@SiO2@NiAl-LDH microspheres display three-dimensional core-shell architecture with flowerlike morphology, large surface area (83 m(2)/g), and uniform mesochannels (4.3 nm). The Ni2+ cations in the NiAl-LDH shell provide docking sites for histidine and the materials exhibit excellent performance in the separation of a histidine (His)-tagged green fluorescent protein, with a binding capacity as high as 239 mu g/mg. The microspheres show highly selective adsorption of the His-tagged protein from Escherichia coli lysate, demonstrating their practical applicability. Moreover, the microspheres possess superparamagnetism and high saturation magnetization (36.8 emu/g), which allows them to be easily separated from solution by means of an external magnetic field and subsequently reused. The high stability and selectivity of the Fe3O4@SiO2@NiAl-LDH microspheres for the His-tagged protein were retained over several separation cycles. Therefore, this work provides a promising approach for the design and synthesis of multifunctional LDH microspheres, which can be used for the practical purification of recombinant proteins, as well as having other potential applications in a variety of biomedical fields including drug delivery and biosensors.