The invention discloses a preparation method of a nanoparticle-modified polyurethane acrylate copolymer resin microemulsion. The method comprises the following main steps: mixing dehydrated polyalcohol, polyisocyanate monomer, hydrophobic nanoparticles, hydroxy acrylate, acrylate monomer, a co-stabilizer and a catalyst to form an oil phase; dissolving a surfactant and an initiator in deionized water, and mixing to form a water phase; and proportionally mixing the oil phase and water phase, carrying out ultrasonic dispersion, and carrying out microemulsion polymerization. The microemulsion polymerization process is utilized to copolymerize the polyurethane and acrylic resin, and the nanoparticles are introduced to obtain the nanoparticle-modified polyurethane acrylate copolymer resin microemulsion. The emulsion has the advantages of high solid content, small particle size, high storage stability and high coating glossiness, can form a compact film material, and can be used in the fields of high-grade coating protection, corrosion-resistant coatings, infrared stealth coatings, wave-absorbing materials, complex top finishing and the like.