Disclosed is a method for preparing a magnetic microsphere for the separation of biological proteins. A magnetic microsphere matrix is treated by formulating and using an appropriate emulsified liquid, and modification of the surface of the magnetic microsphere matrix is realized by emulsion polymerization, thereby obtaining a magnetic microsphere coated with a polyacrylate polymer layer. Said emulsified liquid comprises the following components therein: acyclic acid monoester compounds, acyclic acid glycol compounds, initiators and optionally anionic surface active agents and water. The magnetic microsphere significantly reduces the non-specific adsorption of other proteins, without affecting the joining ability for a specific protein, when used in the separation of biological proteins. A new selection is provided to realize the separation engineering of high protein specificity adsorption.