: Houttuynia cordata Thunb (H. cordata) is a native vegetable colonizing mercury (Hg) mining sites in the southwest of China; it can accumulate high Hg concentrations in the rhizomes and roots (edible sections), and thus consumption of H. cordata represents an important Hg exposure source to human. Here, we studied the spatial distribution, chemical speciation, and stable isotope compositions of Hg in the soil−H. cordata system at the Wuchuan Hg mining region in China, aiming to provide essential knowledge for assessing Hg risks and managing the transfer of Hg from soils to plants and agricultural systems. Mercury was mainly compartmentalized in the outlayer (periderm) of the underground tissues, with little Hg being translocated to the vascular bundle of the stem. Mercury presented as Hg−thiolates (94% ± 8%), with minor fractional amount of nanoparticulate β-HgS (β-HgSNP, 15% ± 4%), in the roots and rhizomes. Analysis of Hg stable isotope ratios showed that cysteine-extractable soil Hg pool (δ202Hgcys), root and rhizome Hg (δ202Hgroot, δ202Hgrhizome) were isotopically lighter than Hg in the bulk soils. A significant positive correlation between δ202Hgcys and δ202Hgroot was observed, suggesting that cysteine-extractable soil Hg pool was an important Hg source to H. cordata. The slightly positive Δ199Hg value in the plant (Δ199Hgroot = 0.07 ± 0.07‰, 2SD, n = 21; Δ199Hgrhizome = 0.06 ± 0.06‰, 2SD, n = 22) indicated that minor Hg was sourced from the surface water. Our results are important to assess the risks of Hg in H. cordata, and to develop sustainable methods to manage the transfer of Hg from soils to agricultural systems.