Recently, the design and preparation of novel functional materials using biomimetic approaches for the high adsorption and precise selective capture of biomolecules have been actively investigated. In this work, molecularly imprinted microspheres (MIMs) with a homogeneous polymer shell anchored onto SiO2 core particles were successfully synthesized via the surface iniferter-initiated polymerization under room temperature in aqueous media. Herein, a clinically relevant immunostimulating hexapeptide from human casein (IHHC) was chosen as a template. Moreover, a novel double imidazolium dicationic ionic liquid with multiple binding sites was synthesized and used as the cross-linker to improve the recognition performance and enhance the adsorption capacity of MIMs simultaneously. The as-prepared microspheres were characterized through various methods. Results revealed that MIMs not only exhibited excellent selective recognition for IHHC but also possessed a high adsorption capacity through the synergistic effect of directional and non-directional interactions, which demonstrated their potential use in the practical application.