Ruoergai uranium deposit is one of the four basic types of uranium ore field in China, where the limestone, silicon limestone and carbonaceous slate are interbedded. The development of faults and steep rock occurrence in this area are the main reasons for hole leakage, collapse, shrinkage and deviation, which also lead to low coring rate, low drilling efficiency and low drilling quality. To solve these drilling problems in Ruoergai is a system engineering, the integrated innovation and management should be started from improving hole safety, drilling efficiency, construction quality, reducing rig moving times and improving removal efficiency to form a set of comprehensive drilling technology system suitable for the complex strata in Ruoergai. This drilling system has demonstration effects for drilling in Western Plateau and deep hole of complex formations.