A series of waterborne polyurethane with PDMS side chain (SiPU) were synthesized using twice-self-emulsifing method. Effects of AEAPS content on properties of SiPU emulsion and films from SiPU emulsion were discussed. The results showed that SiPU emulsion has good stability when AEAPS content in SiPU was less than 10wt%. The PDMS side chains in SiPU were easily enriched to the air-surface of the SiPU films to lower the surface tension and effectively improve the water resistance of the WPU films. When AEAPS content in SiPU reached to 8wt %, SiPU film had good water resistance but the tensile properties were not changed significantly.