A new approach is presented for the adsorption and enrichment of low-abundance protein in mammalian cell extract by using nanostructured surface-imprinted polymers with sufficiently thin shells and high surface-to-volume ratios. Silica nanoparticles with a diameter of 47 nm were used as supports and assistant recognition polymer chains (ARPCs) were used as additional functional monomers. Pig cyclophilin 18 (pCyP18) was chosen as the model protein. The imprinted nanomaterials successfully isolated cloned pCyP18 from a mixture of seven proteins and distinguished natural pCyP18 from cytosol including thousands of proteins. These nanomaterials with high affinity and selectivity offer a great prospect for application.