Fluid transport properties of fault rocks are crucial parameters that affect earthquake nucleation and rupture propagation. In this study, we examined the internal structure, mineral composition and fluid transport properties of fault rocks collected from two shallow boreholes penetrating a granitic rupture zone on the Yingxiu-Beichuan Fault (YBF) that was activated during the 2008 Wenchuan earthquake. Fluid transport properties were measured using water as pore fluid at effective pressures (Pe) ranging from 10 MPa to 165 MPa. Permeabilities of fault rocks exhibit a wide variation from 2.1 × 10− 22 m2 to 4.6 × 10− 17 m2, strongly depending on rock types and overburden pressure. Specifically, at Pe of 165 MPa, the damage zone samples have permeabilities from 5.0 × 10− 21 m2 to 1.2 × 10− 17 m2, and the fault gouges are between 2.1 × 10− 22 m2 and 3.1 × 10− 19 m2. Thus, the YBF consists of a low-permeability fault core acting as fluid barrier, and surrounding high-permeability damage zones acting as fluid conduits. Combining the structural and compositional results and transport data together, we propose that the interplay between cataclasis and fluid-rock interactions controls the hydraulic properties and their response to the fault zone evolution. It is noteworthy that we measured extremely low permeabilities but high porosities and high specific storages for the gouges. The cemented cataclasites, which are inferred to be equivalent to the rocks in which the Wenchuan earthquake nucleated also have low permeabilities, suggesting the fault zone is a potential area for fluid storage and capable of generating high pore pressure at depths. According to our laboratory data, we found fluid pressurization could occur at depths below 2.7 km. We suggest thermal pressurization has played an important role in causing the dynamic weakening of the Wenchuan earthquake.