Waterborne UV-curable polyurethane (WUPU)/ silica nanocomposites were prepared using various types of polyol (PCL, PBA, and PCD) by phase-inversion emulsification. The PCL-WUPU nanocomposite dispersion exhibited larger particles and higher viscosity than the PBA-WUPU and PCD-WUPU nanocomposite dispersions. The TEM analysis indicated that many small silica clusters and a few big silica clusters were distributed in the PCL-WUPU matrix, whereas the silica nanoparticles and the continuous silica network were homogeneously dispersed in the PBA-WUPU and PCD-WUPU matrix, respectively. The DMA analysis demonstrated that the broadening of the tanδ peaks or breadth of segmental motion at lower or higher temperatures were observed for WUPU nanocomposite films, suggesting the different interaction between WUPU and silica. The WUPU nanocomposite films showed increased the storage modulus, Young' modulus, and tensile strength. But for toughness, the PCL-WUPU nanocomposite film exhibited higher improvement than PBA-WUPU and PCD-WUPU due to the silica nanoparticles preferentially, but not exclusively interaction with the hard segment of WUPU. This study provides clues for exploiting silica-polyurethane interactions to control the silica nanoparticles dispersion and tune material properties without surface modification of silica nanoparticles.