The performance of chromatographic media affects the efficiency of purification. In this study, based on a T-type microfluidic droplet generation system, agarose microspheres with large pore size and high load were prepared by adjusting the viscosity of a 4% agarose solution to 70 mPa·s at high temperature. Optical microscopy revealed that the self-made agarose microspheres had a good spherical structure with an average particle size of 82.81 μm and a CV value of 0.0576. Subsequently, the stability and mechanical strength of the self-made agarose microspheres were improved by cross-linking and activation with epichlorohydrin. After the cross-linking and activation, the agarose microspheres were grafted with Protein A to make it have specific adsorption capacity for IgG. The adsorption capacity of the self-made agarose microspheres grafted with Protein A for IgG was 87 mg/g. In the complex serum environment, the agarose microspheres grafted with Protein A still maintained good IgG adsorption capacity and selectivity, demonstrating their potential in practical applications. This study demonstrates the great potential of microfluidic technology in the design and preparation of bio-separation media. By precisely controlling the particle size and pore size of the microspheres, the purification efficiency and selectivity can be significantly improved, providing a new solution for the efficient purification of bio-products.