Natural leather-based materials possess a combination of air permeability, wear resistance, and plasticity. However, conventional leather products have inherent limitations that make them unsuitable for unconventional applications. Therefore, it is necessary to develop new capabilities in order to overcome these limitations. In this study, we explored the conversion of regular leather into a high-strength product with hydrophobic properties through surface engineering. To achieve this, we synthesized polysiloxane-modified fluorinated waterborne polyurethane emulsions as functional coatings using emulsion polymerization. The structure and properties of the treated leathers were characterized using techniques such as Fourier transform infrared, thermogravimetry, X-ray photoelectron spectroscopy, X-ray diffraction, and scanning electron microscopy. The results demonstrated that the synthesized polysiloxane-modified fluorinated waterborne polyurethane successfully penetrated and combined with the fibers of the leather, resulting in excellent hydrophobicity. The water contact angle increased to 124.3°. Furthermore, the tensile strength and tear strength of unfinished leather are 875 N and 114 N, respectively. The application of waterborne polyurethane-derived functional additives as coatings resulted in a significant increase in tensile and tear strength of the leather by 60 N and 16 N, respectively. In addition, the softness of the leather increased from 7.6 mm to 10.09 mm. Overall, the use of this functional waterborne polyurethane coating will contribute to the diversification of leather applications.