A bio-polyol based issued from natural rubber was successfully synthesized for the preparation of waterborne polyurethane (WPU) and hybrid waterborne polyurethane (HWPU). The WPU was prepared by prepolymer process from hydroxyl telechelic natural rubber (HTNR), using dimethylolpropionic acid (DMPA) and hexamethylene diisocyanate (HDI). A series of new HWPUs was successfully synthesized by the sol-gel process, using 3-aminopropyltriethoxysilane (APTES) as a coupling agent. Effects of the amount of APTES (0.8–1.3%wt) on properties of the HWPU were investigated. The WPU and HWPU with APTES content ranging from 0.8 to 1.0%wt showed well-dispersed particles with a long shelf life exceeding 3 months. The particle size increased with APTES content. In addition, the HWPUs showed increasing zeta potential with APTES content. The morphology and shape of particles were observed from Transmission Electron Microscopy (TEM) imaging. The chemical structures in WPU and the series of HWPUs were confirmed by FT-IR. The tensile strength of HWPU was improved on incorporating Si–O–Si linkages into the WPU backbone through a sol-gel process. Moreover, effects of the amount of nano-silica (0–15%wt) on properties of the HWPU/silica were investigated. TEM images demonstrated miscibility and specific interactions between HWPU and the dispersed nano-silica particles. The morphology of HWPU/silica films was characterized by Scanning electron Microscopy (SEM), and the elemental analysis of surfaces was carried out by Energy Dispersive X-ray Spectroscopy (EDX). Additionally, nano-silica content enabled the hydrophobicity of HWPU/silica films, leading to water repellence and good water resistance. Moreover, the mechanical and thermal properties were significantly improved on increasing nano-silica content. The investigation demonstrated that using HTNR polyol in the formulation of a new HWPU dispersion is an environmentally friendly alternative, in which performance of the film is improved on adding nano-silica via a sol-gel process. The novel films have potential for coating applications.