Silicon-containing polyurethane pre-polymer (IPDI-Si) was prepared from γ-mercaptopropyltriethoxysilane (TMPS), isophorone diisocyanate (IPDI) and hydroxyethyl methacrylate (HEMA). Then, a series of silicon-containing polyurethane modified acrylic resins with different additive amount of IPDI-Si were prepared with isopropyl alcohol (IPA) as solvent and 2,2'-azobis(2-methylpropionitrile) (AIBN) as initiator. Finally, a series of waterborne acrylic resin dispersions were prepared by emulsification with triethylamine as neutralizer in the presence of water. The dispersions and cured resin coatings were characterized by FTIR, XPS, TGA, TEM and SEM. And the storage stability of the dispersion, and the hardness, adhesion and other properties of the coatings were tested. The results showed that when the additive amount of IPDI-Si was 3% (based on the total mass of polymerized monomers, the same below), the prepared dispersion had better storage stability and excellent resin coating performance. The prepared coating exhibited good compactness. The hardness was 2 H and the adhesion was grade 1. The water contact angle was 96.1 °. And the tensile strength of the coating was 9.4 MPa and the elongation at break reached 385%. The thermogravimetric analysis demonstrated that the temperature at 10% weight loss (T10%) of the coating reached 306.1 ℃