Bio-based coating materials have received increased attention because of their low-cost, environmentally friendly, and sustainable properties. In this paper, a novel coating material was developed to coat ureas using bio-based coating material derived from liquefied eggplant branches to form controlled-release ureas (CRUs). Also, the optimum proportion of liquefier was studied. Furthermore, dimethyl siloxane was used to modify liquified eggplant branches to make them hydrophobic, resulting in hydrophobic controlled-release ureas (SCRUs). This hydrophobic-enabled coating is environmentally friendly and highly efficient. The products were characterized by specific scanning electron microscopy, energy-dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, and the water contact angles of CRUs and SCRUs were determined. The nutrient-release characteristics of the SCRUs in water were determined at 25 °C and compared with those of CRUs. The results showed that the modification with dimethyl siloxane reduced the N release rate and increased the longevity of the fertilizer coated with hydrophobic bio-based coating material. In addition, organosilicon atoms on the SCRU surface also block the micro-holes on the coating and thus reduce the entry of water onto the coating. The results suggest that the new coating technology can create a hydrophobic surface on bio-based coating material and thus improve their controlled-release characteristics.