Based on the Wenchuan Earthquake Fault Scientific Drilling Project (WFSD), we first investigated the distribution of the total mercury (THg) from 600 m to 1035 m of WFSD Hole-1 core (WFSD-1). The concentrations of THg in the fault gouge are significantly higher than in the sandstone, shale, siltstone, and cataclasite in WFSD-1. The THg concentrations in the main seismic fault zone range from 9.9 to 73.5 ng/g while those under the main fault range from 20.5 to 36 ng/g. To determine the source of Hg, typical rocks from different depths were chosen for Hg isotope analysis. The results show that δ202Hg in the main seismic fault zone range from − 0.11‰ to − 2.68‰, and, below the seismic fault zone, δ202Hg are from − 0.64‰ to − 1.33‰. The seismic fault rocks are more enriched in THg and have a larger variation of δ202Hg compared to the other rocks. Mercury has different isotopic compositions and fractionation mechanisms in the fault zone, which are mainly affected by the earthquake and the fluid. The mercury isotope compositions reflect the fluid activities at the main fault zone. We demonstrate that mercury stable isotope ratios could serve as an effective tool for tracing mercury sources and monitoring and predicting earthquakes.