The invention discloses water-based organic silicon modified cationic acrylic resin and a synthesis method. The water-based organic silicon modified cationic acrylic resin is prepared from the following raw materials: a monomer, a functional monomer, a solvent, acid, a chain transfer agent and an initiator, wherein the monomer comprises, by weight, 100-400 parts of methyl methacrylate, 5-50 partsof butyl acrylate and 20-200 parts of styrene, the functional monomer comprises, by weight, 10-100 parts of vinyltriethoxysilane, 20-200 parts of dimethylaminoethyl methacrylate and 30-250 parts of hydroxyethyl acrylate, the solvent comprises, by weight, 100-400 parts of propylene glycol monomethyl ether, 50-400 parts of absolute ethyl alcohol and 20-200 parts of N, N-dimethylformamide, the acid is 5-60 parts by weight of lactic acid, the chain transfer agent is 1-50 parts by weight of a methyl styrene linear dimer, and the initiator is 1-50 parts by weight of azodiisobutyronitrile. The invention solves the fundamental problems of unsatisfactory hardness, transparency, solvent resistance and other properties, high cost and the like of the traditional water-based wood paint, can completelyreplace the oil-based PU wood paint, and can generate great advantages for environmental beautification without losing the properties under the large situation of environmental protection.