The formations of Wenchuan Earthquake Fault Scientific Drilling Project (WFSD) are extremely complicated. They are strong broken, high water sensitive and high stressed, which resulted in high difficulty of drilling operation. On the basis of theoretical analysis, some countermeasures were put forward to solve the problems. During the drilling operation of several boreholes of Wenchuan Earthquake Fault Scientific Drilling Project, we selected and evolved four different drilling fluid systems, included modified sulfonated, LBM-GLA and potassium lime polysulfonated drilling fluid systems, which have been good effective in applications. Also, this paper summarized the characteristics and application scope of all the drilling fluid systems. In addition, some experiences and suggestions on drilling fluid application for the deep hole with complex formation are put forward.