Waterborne polyurethane prepolymer (WPU), polyacrylate (PA), silicone modified waterborne polyurethane prepolymer (SiWPU) and polyacrylate (SiPA) were synthesized using isophorone diisocyanate (IPDI), γ-aminopropyltriethoxysilane (KH550), methyl methacrylate (MMA) and γ-(methacryloyloxy)propyltrimethoxysilane (KH570) as main raw materials. Then, silicone acrylate double modified waterborne polyurethane (SiWPUA) emulsions were synthesized by interpenetrating network polymerization using WPU, SiWPU and SiPA as raw materials. The effects of PA addition amount, SiPA addition amount and SiWPU addition amount on the water resistance of the emulsion films were investigated by measuring water absorption rate and water contact angle and the mechanism was analyzed. The results showed that the water absorption rate of SiWPU-40%-SiPA-37.5% (40% is the content of SiWPU based on the total mass of WPU and SiWPU, the same below, and 37.5% is the mass fraction of SiPA in the system) film was reduced from 37.4% before modification to 6.8%, the contact angle was increased from 56.8° to 86.4°, and pencil hardness was increased from HB to H. Thermogravimetric analysis demonstrated that the Tmax (the temperature at which the decomposition reaction occurs) of SiWPU-40%-SiPA-37.5% was 412.4℃, higher than that of WPU (340.2℃). TEM results revealed that the modified latex particles had a core-shell structure. SEM of film section and XRD results showed that both PA and silicone modification increased the crosslinking degree of the polymer.