Surface molecular imprinting for proteins is an emerging cross-field of molecular imprinting engineering and functional materials. In this contribution, we report a novel design of magnetic two-dimensional molecularly imprinted polymers (2D-MIPs) for the high recognition and separation of proteins. Bovine serum albumin-surface-imprinted polydopamines were prepared on the surfaces of the magnetic Fe₃O₄–graphene oxide hybrid to form magnetic 2D-MIPs for proteins. The 2D Fe₃O₄–graphene oxide substrate possesses a dominant surface-to-volume ratio in comparison to 3D spherical substrates with the same volume. These materials are sensitive to a magnetic field and can be easily separated using an external magnet. The binding experimental results of bovine serum albumin on magnetic 2D-MIPs and real sample analysis demonstrated the high recognition specificity, selectivity, accessibility and convenient separation of 2D-MIPs for template protein. The design and synthesis of magnetic 2D-MIPs provide a new perspective for the surface molecularly imprinted materials with potential in the recognition and separation of proteins.