To further improve the hydrophobic and thermal properties of fluorinated polyurethane (FPU), we initially prepared the fluorine-and silicon-containing pendant groups’ diols (DEFA and DESiA) by Michael addition reaction. Next, we synthesized a series of co-modified polyurethane nanocomposite (TPFPU-SiO2) latexes by terminal and pendant fluoroalkyl segments via varying the additive amount of silica sols. Structure and performance properties of the target materials were characterized by IR, TEM, TGA, DSC, XRD, XPS, SEM, AFM, and contact angle measurements. Results showed that with the increase in silica sols dosage, the mean particle size of the TPFPU-SiO2 latexes was increased and their emulsion stability gradually decreased. The thermal stability of the TPFPU-SiO2 films were gradually increased and hydrophobicity of the TPFPU-SiO2 films increased first and then slightly decreased. The maximum water contact angle on the TPFPU-SiO2 films was 119.8° and the lowest water absorptivity was 2.49%. Thus, these novel fluorinated polyurethane nanocomposite latexes can find valuable applications in heat-resistant and anti-fouling coatings.