A series of polyurethaneurea (PUU) aqueous dispersions were prepared via a prepolymer process from polyester polyol, alpha,omega-dihydroxypolyl[(3,3,3-trifluoropropyl) methylsiloxane] (PTFPMS), dimethylolpropionic acid, isophorone diisocyanate, and ethylenediamine. These anionic-type aqueous dispersions were stable at the ambient temperature for more than 6 months, with particle sizes ranging from 69 to 127 nm. For these aqueous dispersions, the surface tension decreased with increasing PTFPMS content, but the particle size increased with a maximum value. The film prepared from the PUU aqueous dispersion consisting of 5 wt % PTFPMS (APU-FS-5) exhibited excellent waterproof performance. Furthermore, the tensile strength of the APU-FS-5 film increased nearly 3 times compared with that of the PUU film without PTFPMS, whereas the elongation at break only decreased a little; this indicated that the water-resistant and mechanical properties could be enhanced markedly and simultaneously for the PUU films containing both silicon and fluorine groups. The experimental results showed a high degree of hydrogen bonding for urea groups and an increased microphase-separation degree between the hard and soft segments in the PTFPMS-modified system, which resulted in the excellent mechanical properties of these films.