The hydrophobic modification effect and an appropriate cost of waterborne polyurethane are regularly pursued targets of researchers. To further enhance the hydrophobic modification effect of the terminal fluoroalkyl group and control the cost, a fluorine-containing pendant group diol (DEFA) was first synthesized by the Michael addition reaction of diethanolamine (DEOA) and dodecafluoroheptyl methacrylate (G04). Next, a series of modified polyurethane latexes (TPFPU) by the terminal fluoroalkyl segments (perfluorohexyl ethanol, S104) and the pendant fluoroalkyl segments (DEFA) were synthesized by varying the DEFA dosage. Structure and performance properties of the resultants were characterized by IR, 1H NMR, TEM, TGA, DSC, XRD, XPS, SEM, AFM and contact angle measurements. Results confirmed that the product could be successfully prepared using the present method. With the increase in DEFA dosage, the average particle size increased gradually. Thermal stability was enhanced and small regional crystals were probably produced. XPS and AFM results demonstrated that the degree of microphase separation and film roughness were increased with the increase in DEFA amount. Hydrophobicity of the TPFPU’s film was also increased with the increase in DEFA dosage, and it could be guaranteed when the mass content of S104 and DEFA was larger than 17.0 wt% in total mass of raw materials, which demonstrates that the terminal and pendant fluoroalkyl groups have the favorable synergistic effect on the properties of polyurethane.