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Drilling in an active fault quickly after a large earthquake is an effective way to study earthquake mechanisms. In order to better understand the mechanical, physical, and chemical characteristics of the faults that ruptured during the 2008 Wenchuan earthquake (Mw 7.9), six boreholes were drilled on the two main strands (Yingxiu–Beichuan and Guanxian–Anxian faults) by the Wenchuan earthquake Fault Scientific Drilling project (WFSD). This paper focuses on the cores from the WFSD-3 borehole which drilled across the Guanxian–Anxian fault. A detailed petrological study shows that fault gouge and fault breccia are developed in the WFSD-3 cores in the Late Triassic Xujiahe Formation. The thicknesses of fault gouge range from ~1 mm to ~2.3 m. According to the characteristics of the fault rock combinations and their distribution, at least 22 subsidiary fault zones were recognized in the WFSD-3 cores. The Guanxian–Anxian fault zone is composed of fault rocks from 1192 to 1250.09 m depth, with a real thickness of ~50 m (~60 m thick in the WFSD-3 cores), and an actual damage zone of ~160 m (~980–1192 m depth in the WFSD-3 cores), and shows characteristics of multiple high-strain fault cores. The damage zone is only present in the hanging wall. The actual total thickness of the Guanxian–Anxian fault zone is ~210 m. Based on the analyses of comprehensive logging data, characteristics of the fault gouge, and seismic fault structures, the principal slip zone for the Wenchuan earthquake is identified in the black fault gouge at 1249.95 m depth in the cores, which lies almost at the bottom of the Guanxian–Anxian fault zone, and is also confirmed by surface rupture zone observations. The slip plane of the Wenchuan earthquake is a low-angle thrust fault with a dip angle of ~38° as estimated from the results of the WFSD-3 core analyses. The results from WFSD-1 showed that the Yingxiu–Beichuan segment is a high-angle thrust fault striking NW with a dip angle of ~65°. These two fault segments have different thicknesses and fault structures, which may suggest different faulting mechanisms and evolution history. © 2015, Springer-Verlag Berlin Heidelberg.