The invention belongs to the technical field of coating, and discloses a waterborne alkyd resin modified by epoxy resin and organic silicon and its preparation method. The waterborne alkyd resin modified by epoxy resin and organic silicon is prepared from, by mass percent, 3-6% of epoxy resin, 12-16% of half-dry plant oil, 12-16% of tung oil, 2-5% of benzoic acid, 14-18% of polyhydric alcohols, 15-20% of organic binary acid, 3-5% of aromatic disulfonic acid (salt), 2-4.2% of alkenyl-containing organic silicon monomer, 0.005-0.015% of alcoholysis catalyst, 0.01-0.05% of esterification catalyst, and 22-26% of cosolvent. The waterborne alkyd resin has good storage stability, and can be applied to water-based coating; the waterborne alkyd resin shortens the drying time of paint film and improves the water durability and weather fastness of the paint film.