The inherent large number of hydroxyl groups of silica poses strong hydrophilicity, resulting in poor dispersibility in the natural rubber matrix. Here, the silica’s surface was hydrophobically modified with [3-(triethoxysiliconyl) propyl] tetrasulfide (Si69) to improve the dispersibility and reinforce the mechanical properties of silica/natural rubber composites. The structure and morphology of modified silica were characterized by Fourier infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), X-ray electron spectroscopy (XPS), nuclear magnetic resonance spectroscopy and the contact angle. Further, the mechanical properties, dynamic mechanical properties and morphology of silica/natural rubber composites were studied with a universal electronic tension machine, dynamic thermal mechanical properties analyzer (DMA) and scanning electron microscope (SEM). The experimental results show that the Si69 was successfully grafted onto the surface of silica, thereby significantly improving the water contact angle (a 158.6% increase) and enhancing the mechanical properties of modified silica/natural rubber composites.