The Yingxiu–Beichuan fault zone (YBFZ) has long been active and experienced repeated large earthquakes. The physicochemical properties of the deep fault zone (>1000 m) are the key to understanding the deformation mechanism of large earthquakes. This study uses rock magnetic, microstructural, and geochemical analyses of representative samples exposed in FZ1681 within the Wenchuan Earthquake Fault Scientific Drilling borehole 2 (WFSD-2) cores. Fault gouge and fault breccia have higher magnetic susceptibility values than wall rocks, and they contain abundant paramagnetic minerals and small quantities of magnetite and monoclinic pyrrhotite. The magnetite and monoclinic pyrrhotite in the fault gouge were mainly formed by coseismic frictional heating, indicating that large earthquakes with frictional heating temperatures of ~500–900℃ once occurred in the YBFZ. The seismogenic and coseismic environment was reducing with a relatively high sulfur content. The monoclinic pyrrhotite in the fault breccia was formed mainly by low-temperature hydrothermal fluid. This indicates that the fault zone experienced reducing and low-temperature (<400℃) hydrothermal fluid with a relatively high sulfur content after the earthquake. The YBFZ, which experiences frequent large earthquakes, is weakly oxidizing environment at different depths, but the effect of the low-temperature hydrothermal fluid is weaker at depth.