Waterborne polyurethane polyacrylate emulsion (WPUA) was synthesized with thermotolerant polyester diol (NCL), 4,4’-dicyclohexyl methane diisocyanate(HMDI) and methyl methacrylate (MMA) as raw materials, using both carboxylic acid and sulfonate as hydrophilic chain extender agent. WPUA with zero VOC and no triethylamine was prepared by solvent-free method to meet the requirements of cigarette packaging industry. The WPUA emulsions and films were characterized by FT-IR, transmission electron microscope(TEM), partical size analysis and thermogravimetric analysis(TGA). The effects of different kinds of isocyanates, polyalcohol and chain extender on thermal stability of the WPUA films were investigated. The results showed that the average particle size of the emulsion was reduced due to the addition of aliphatic diamine sulphonate(AAS). TGA results showed that the decomposition temperature of WPUA5 film synthesized by NCL, HMDI and novel chain extender hydroquinone bis(β-ethyl) ether(HQEE) was higher than that of WPUA2 film synthesized by polycaprolactone diol(PCL), isophorone diisocyanate(IPDI) and 1,4-Butanediol(BDO), the decomposition temperature increased by 60.96℃, 69.37℃, 139.70℃ when the mass loss rate of WPUA film was 20%, 30%, 50%. And the crystallization and glass transition temperature (Tg) of polyurethane both increased with the enhancement of the symmetry of molecules.