The first hole of the Wenchuan earthquake Fault Scientific Drilling (WFSD-1) was started on Nov. 6, 2008 as a rapid response to the May 12, 2008 Wenchuan earthquake (Mw 7.9), which slipped along the Longmen Shan fault on the eastern margin of the Tibetan Plateau. WFSD-1 was drilled to a depth of 1201.15 m and intersected the presumed active fault zone at a depth of 590 m (FZ590), which contains the maximum value of fracture density and fresh fault gouge. Here we characterized fault rocks of FZ590 by conducting XRD analyses with cohesive and non-cohesive rock samples collected from WFSD-1 borehole cores. The results indicate that a clay anomaly zone is located in the FZ590 fault zone. The slight enrichment of smectite distributed in fresh fault gouge implies that there is a fault-related authigenic clay formation. In addition, the location of the slight enrichment of smectite is consistent with the plausible active slip zone determined by previous results, adding confidence to the supposition that the principal slip zone (PSZ) of the 2008 Wenchuan earthquake is located at a depth of 589.2 m and situated at the lithological boundary of the Neoproterozoic Pengguan Complex and Triassic Xujiahe Formation. The tiny clay anomaly signal captured from borehole cores implies that low frictional heat was generated by coseismic slip, which drives only slight authigenesis processes. Thus, other dynamic weakening mechanisms, such as thermal pressurization may be involved in the fault zone of the Yingxiu–Beichuan fault during 2008 Wenchuan earthquake.