In this study, environmentally friendly UV-curable polyester-based waterborne polyurethane (WPU)/functionalized silica nanocomposites were successfully prepared. The functionalized silica was combined with WPU by chemical bonds and existed as effective cross-link points to form composites. Because of the existence of organic molecule chains from the functionalized silica, the compatibility of WPU with silica was improved obviously. This makes the composite latex possesses certain stability when the silica content rose up to 17.5 wt %. The composite latex particles kept the structure where the functionalized silica was covered by WPU during the film formation process, which could greatly decrease the aggregation of silica. What's more, the existence of functionalized silica improved thermo-stability, hardness, and water resistance of composite films effectively and the composite films possessed good transparency.