Agar microspheres were prepared by water–oil emulsification and cross‐linked under alkaline condition. The thermoresponsive hydrophobic copolymer, poly(N‐isopropylacrylamide‐co‐lauryl methacrylate‐co‐acrylamide), was grafted on the agar microspheres via atom transfer radical polymerization. The agar microspheres grafted with copolymers were characterized by light microphotography, elemental analysis, Fourier transform infrared spectroscopy, scanning electron microscopy, and X‐ray photoelectron spectroscopy. The chain lengths and hydrophobic monomer ratio of the grafting linear polymer had significant effects on the hydrophobicity and adsorption capacity of agar microspheres at different temperatures. The thermoresponsive microspheres were used for separation of proteins and showed binding and release behavior by change of temperatures without change in mobile phase composition. Thus, we suggest thermoresponsive agar microspheres as an alternative separation media for all‐aqueous bioseparations.