A series of waterborne polyurethanes (WPU) with crosslinked siloxane were obtained through introducing 3-(2-aminoethylamino)propyldimethoxymethylsilane (APTS) into WPU by in situ polymerization. The properties of WPU modified by APTS were studied through a variety of experimental methods. The water contact angle of the WPU coating surface increased from 64° to 86°, and the water resistance reduced to 3.90% when 3 wt% APTS was added, which improved the coating surface hydrophobicity. Firstly, Fourier transform infrared (FT-IR) and 1H-NMR spectra demonstrated the successful incorporation of APTS to polyurethanes and completed the hydrolytic condensation reaction-generated Si–O–Si crosslinking structure. Furthermore, the surface energy of the membrane was reduced when the crosslinking structure migrated and enriched on the surface of film. Besides, the crosslinking structure was abundant, and the distribution of siloxane in WPU was more uniform.