Bio-based polyurethane (BPU) has been developed using a castor oil/poly(ε-caprolactone) hybrid polyol, and hydrophobic BPU ultrafine fibers containing modified silica (m-silica) were successfully fabricated using an electrospinning process. The successful modification of the silica nanoparticles and the synthesis of BPU composites were confirmed by Fourier transform infrared spectroscopy data. The rheological properties of the BPU solutions and BPU/m-silica suspensions were investigated to characterize any structural changes induced by incorporation of the m-silica and to control the electrospinning parameters. The rheological analysis revealed that a network structure existed between the BPU and m-silica, which led to a remarkable improvement in the mechanical properties and thermal stability. A morphological change in the ultrafine fibers on incorporation of the m-silica nanoparticles was also observed: the average fiber diameter of the hybrid ultrafine fibers decreased with increasing m-silica content. Furthermore, the m-silica nanoparticles resulted in a change in the effective surface wettability of the BPU ultrafine fibers resulting in a change from hydrophilic to hydrophobic behavior. The present BPU/m-silica ultrafine fibers, which have improved rheological properties, hydrophobic surface, mechanical properties, and thermal stability, may be a potential candidate to replace petroleum-based polyurethane membrane, in the field of biofilters, eco-friendly textiles, and biomedical engineering.