In this work, we report a facile approach for imprinting protein based on self-polymerization of dopamine in the presence of template protein on the Fe3O4 nanoparticles (NPs) surface. Dopamine, commonly known as a neurotransmitter, is also a small-molecule mimic of the adhesive proteins of mussels. Self-polymerization of dopamine can produce a thin polydopamine (PDA) layer on Fe3O4 NPs surface. During the self-polymerization of dopamine, some template protein molecules were embedded in the PDA layer. After the removal of these embedded protein molecules, the protein imprinted sites are created. The prepared imprinted Fe3O4@PDA NPs shows high binding capacity and acceptable specific recognition behavior towards template proteins.