The deep Dongying to Shahejie formations in the Jidong Oilfield are prone to unstable shale formations, with well-developed bedding and fractures. During the drilling process, there are problems with wellbore instability such as collapse and falling blocks, which affect the exploration and development process. The whole rock mineral analysis shows that the mineral composition of deep mud shale is mainly composed of clay minerals, with an average content of 43.56%. The average content of illite/montmorillonite mixed layer accounts for 60.29%. The recovery rate of shale in clean water is 56.5–96%, and the expansion rate is 13–23.61%. Scanning electron microscopy shows that the mud shale has well-developed microcracks, micropores, and micropores, with pore distribution ranging from 4 to 200 nm, mainly at the nanoscale pore size. Through CT scanning imaging experiments, it was found that the formation process of shale fractures can be divided into four steps, namely microcrack initiation, expansion (widening), expansion (extension), and penetration, forming a three-dimensional spatial crack. The contact experiment with 5% KCl solution shows that only improving the inhibitory effect of external fluids cannot effectively prevent the opening of shale fractures. Triaxial tests and shear tests along structural planes indicate that weak structural planes are more sensitive to drilling fluids. Research has shown that for unstable shale formations, improving sealing performance is the key to wellbore stability. Two sets of chemical wellbore stable drilling fluid systems, namely reverse osmosis low free water and potassium salt high-temperature resistant nano micron sealing, have been formed. The two drilling fluid systems have increased the shale sealing rate by 33–46% and the rock mechanical strength retention ability by 25.5%. The on-site application has achieved good results, providing technical countermeasures for safe drilling of deep shale in Nanpu.