The invention discloses a preparation method of water-soluble organic silicon-modified acrylate resin. The preparation method comprises the steps of carrying out free radical polymerization on an unsaturated monomer containing an ethylidene-urea structure and multiple allyl monomers in an alcohol or alcohol ether solvent, and synthesizing acrylate resin containing an ethylidene-urea active side group; adding epoxy siloxane and carrying out ring-opening reaction with an epoxy group by using secondary amine on the ethylidene-urea structure; and adding organic amine for neutralization and salt formation. The preparation method of the water-soluble organic silicon-modified acrylate resin is simple; a water-soluble thermosetting coating prepared from the modified resin, water-based amino resin and related assistants is good in storage stability; and the cured film is excellent in hardness, water resistance, boiling resistance and ethanol tolerance, and can be widely used as a protective coating for glass and metals.