Waterborne polyurethane emulsions were synthesized with isophorone diisocyanate(IPDI), dihydromethyl propionic acid(DMPA) and poly-ε-caprolactone glycol(PCL), and then reacted with hydroxy-ethyl acrylate(HEA) and 3-aminopropyltriethoxylsilane(APTES) to cap the terminal -NCO groups. The polyurethane emulsions were used to copolymerize with acrylates to synthesize the modified waterborne polyurethane-acrylate hybrid emulsions. The structure, thermal stability and crystallinity of modified polyurethane were studied by FTIR, TG, XRD and the mechanical properties of modified polyurethane films was also investigated. The results show that crystallization of the modified waterborne polyurethane decreases and thermal stability is improved. When the mass fraction of acrylate is 20% and APTES content is 15%, tensile strength of the modified polyurethane films can reach 23.9MPa and elongation at break is 247%.