Molecularly imprinted mesoporous materials (MIMs) were synthesized to improve the adsorption performance of Cytochrome c (Cyt c) by using an imidazolium-based amphiphilic ionic liquid 1-octadecyl-3-methylimidazolium chloride (C₁₈MIMCl) as surfactant in aqueous solution via the epitope imprinting approach. The surface-exposed C-terminus nonapeptide of Cyt c (residues 96–104, AYLKKATNE) was utilized as the imprinted template. The nitrogen adsorption-desorption, thermo-gravimetric analysis, and transmission electron microscopy verified the successful preparation of MIMs with ordered mesoporous structure. The adsorption isotherm studies showed that the obtained MIMs exhibited superior adsorption capacity toward Cyt c of 86.47 mg·g⁻¹ because of the high specific surface areas of 824 m²·g⁻¹, and the appropriate pore size promoted the mass transfer of Cyt c, causing a rapid adsorption equilibrium within 20 min. Furthermore, these MIMs still remained excellent selectivity and recognition ability according to the selective as well as the competitive adsorption studies, suggesting that the molecularly imprinted mesoporous materials is expected to be used in the field of highly efficient separation and enrichment of proteins.