During the drilling process in shale formations, issues such as wellbore instability, hydration expansion, and the formation of nanoscale microcracks are prominent, making it difficult for traditional water-based drilling fluids to achieve effective plugging. For this purpose, hydrophobic nano silica plugging agents and drilling fluid formulations have been designed and developed to meet the drilling requirements of shale formations. Hydrophobic modification of hydrophilic nano silica was carried out using silane coupling agent. The modified hydrophobic nano silica plugging agent was introduced into the water-based drilling fluid system. The drilling fluid treatment agent was optimized by comparative experimental method to develop the water-based drilling fluid formula. The influence of hydrophobic nano silica on the performance of water-based drilling fluid was evaluated through rheological, filtration, lubricity, expansion, temperature and salt resistance experiments. The research results show that the apparent viscosity and plastic viscosity of this hydrophobic nano silica drilling fluid can reach 41.5 mPa·s and 28 mPa·s, the filtration loss is 7.2 mL, the slider resistance coefficient is 0.2035, and the expansion is as low as 12 mm or less. It can work in harsh environments such as 140℃ or 8% NaCl. This indicates that the developed hydrophobic nano silica plugging agent has excellent inhibitory effect, and the drilling fluid formula can meet the needs of shale formation drilling work.