Mercury isotopes display large mass-dependent fractionation (δ²⁰²Hg) and mass-independent fractionation (Δ¹⁹⁹Hg) in the land-ocean-atmosphere system. However, the Hg isotopic composition in interior reservoirs (e.g., crust and mantle) remains poorly known. The arc lower crust between the deep mantle and the shallow crust records information from both layers simultaneously. Our study presents the first Hg isotopic dataset of the lower crustal rocks from the Jijal and Chilas Complexes of the exhumed Kohistan arc in northwestern Pakistan. These rocks have average Hg concentrations (2.21 ± 3.65 ppb, 1 standard deviation [SD]), δ²⁰²Hg (−0.91‰ ± 0.47‰, SD), and Δ¹⁹⁹Hg (0.02‰ ± 0.04‰, SD) that can be used to represent the Hg abundance and isotopic composition of the lower crust of subduction zones. These values are distinct from estimates for the juvenile lower crust of the Central Asian Orogenic Belt (total Hg concentration: 6.12 ± 4.86 ppb; δ²⁰²Hg: −2.5‰ ± 0.8‰; Δ¹⁹⁹Hg: 0.06‰ ± 0.07‰, SD). We demonstrate that metasomatism in the mantle source and assimilation of Hg from the upper continental crust are two mechanisms responsible for the difference in Hg abundance and isotopic composition in the lower continental crust at different tectonic settings. Our study fills a Hg knowledge gap in the lower crust, and provides key support for using Hg isotopes for constraining crust-mantle interactions.