In this work, super-paramagnetic interface molecularly imprinted microspheres (MIMIMs) were prepared using an immunostimulating hexapeptide as template via photo-initiated Pickering emulsion polymerization by the self-assembly of the template-immobilized silica nanoparticles at the oil-water interface under room temperature. The whole experiment process was tracked and analyzed by various characterization methods. Results manifest that the obtained MIMIMs showed excellent recognition property and rapid-efficiency separation for template peptide due to their accessible imprinted sites and desired magnetic susceptibility. Moreover, MIMIMs were used in competitive rebinding and reusability tests, which demonstrated their potential application in the enrichment of IHH and sustainable performance in resource-saving.