The imidazolium cation was chosen as protein selective affinity group and a kind of ionic liquid magnetic microspheres was developed by immobilizing imidazolium cations onto the surface of silica-coated magnetic microspheres to form imidazolium ionic liquid modified magnetic microspheres (Fe3O4@SiO2@IL). Elemental analysis data confirmed and quantified the immobilization of the ionic liquid. The most distinct feature of the magnetic microspheres is the high hemoglobin binding capacity (more than 2 g of hemoglobin per gram of beads) owing to the covalent coordination between the imidazolium cation and the iron atom in the heme group. Moreover, imidazolium ionic liquid modified magnetic microspheres (Fe3O4@SiO2@IL) have selective affinity to proteins with different charges due to their own isoelectric point. Therefore, the magnetic microspheres can selectively capture protein under an appropriate solution pH. Furthermore, the short processing time (15 min) is suitable for purifying unstable proteins. In addition, the separating and recycling of the magnetic microspheres by using a magnet is quite convenient.