Fault zones record a series of faulting events that have occurred under different physical conditions during their evolution. Therefore, it is essential to understand the internal structures of fault zones in order to better understand the mechanical behavior of faults. The internal structure of the Wenchuan earthquake fault zone that prevailed at the Bajiaomiao outcrop and in the WFSD-1drilling cores, located along the southern segment of the Yingxiu–Beichuan surface rupture in the Hongkou area, is described in details in this paper. Based on field surveys, X-ray diffraction analysis, microstructure and analysis of the drilling cores, an ~ 240 m-wide fault zone was confirmed as the Yingxiu–Beichuan fault zone (YBF) at the Bajiaomiao outcrop, corresponding to the ~ 100 m fault zone in the WFSD-1 drilling cores. Fault rocks, including fault breccia, fault gouge and cataclasite were identified in both the outcrop and drilling cores, while pseudotachylyte was only present at the outcrop. Two different types of gouge veins, formed by thermal pressurization and fluidization respectively, are observed in this area. The YBF possesses the characteristics of a multiple core model, and consists of 5 different fault rock units. From top to bottom, these are cataclasite zone, black fault gouge–breccia zone, gray fault breccia zone, dark-gray fault breccia zone and black fault gouge–breccia zone. Outcrop investigation and drilling core research show that the slip zone of the Wenchuan earthquake does not completely follow the ancient fault slip zone. The Wenchuan earthquake fault is a high angle thrust fault which crosses the YBF obliquely. The multi-layered fault rocks displayed in the research area might indicate that the YBF comes from the long-term fault activity and evolution over the last ~ 15–10 Ma.