Protein imprinting is still a challenge due to the low binding kinetics and poor binding selectivity. In this study, a facile method of the preparation of magnetic molecularly imprinted polymers (MIPs) for selective protein separation was reported. Carboxyl group functionalized FeO nanoparticles (NPs) were synthesized using a solvothermal method. After pre-assembly of caroxyl group functionalized FeO NPs and template protein lysozyme (Lyz) to form Lyz-FeO complex, magnetic MIPs were synthesized by a sol-gel process of 3-aminopropyltriethoxylsilane and tetraethyl silicate with Lyz-FeO complex incorporated. Then FeO-MIPs particles with magnetic response could be collected by simple crush of bulk polymers. This preparation process avoid the need of high dilution of monomer for anti-agglomeration in the surface imprinting, and large amount of solvent is spared. The morphology and structure property of the prepared magnetic NPs were characterized by transmission electronic microscopy, Fourier transform infrared spectroscopy, and vibrating sample magnetometer. Binding experiments were carried out to evaluate FeO-MIPs particles' binding performance and selectivity. And results showed fast binding kinetics, high binding capacity, and favorable specific recognition behavior toward template protein, which is due to the role of carboxyl group functionalized FeO NPs as both magnetic source and importantly as co-functional monomer incorporated in the polysiloxane imprinting system. Real egg white sample tests demonstrate good separation effect. This report provides a possibility of the selective separation of protein in complex matrix.