Carbon fiber (CF) surface sizing coatings with molecularly dual interpenetrating three-dimensional cross-linked network structure were designed by varying the content of poly(diaminosiloxane) groups grafted onto branch chains of cross-linked polyester/polyether waterborne polyurethane (WPU). The synergistic modification of intramolecular cross-linker (TMP) and poly(diaminosiloxane) coupling agent introduced excellent organosiloxane chains into WPU system, and the hydrolytic condensation reaction of polysiloxanes further enhanced cross-linking network density. The hydrophobicity and thermal stability of WPU had been improved by the introduction of polysiloxanes and establishment of cross-linked networks. The temperature of polyurethane at thermal weight loss T5% and Tmax were increased from 219.8 °C and 411.5 °C to 273.2 °C and 430.2 °C, respectively. Compared to untreated CF, the surface free energy and polarity component of WPU treated CF increased by a factor of 1.6 and 3.5, and tensile strength of fiber increased by 20.3 %. The surface migration characteristics of polysiloxanes and the increased density of dual interpenetrating cross-linked network further enhanced effectiveness of WPU coatings in improving surface roughness of fibers and repairing defects. The polysiloxanes with low surface tension and surface energy characteristics as well as polar chains and active groups in WPU collectively enhanced the wettability and chemical reactivity of CF interface. Polysiloxans branched cross-linked polyester/polyether WPU had the potential to optimize the utility of CF in energy vehicle drive shafts and high-speed rail trains vibration damping devices, and contributed to the innovation of environmentally friendly sizing coatings.