Contents of total Hg and Hg fraction, organic matter, pH, grain size and chemical composition were measured to investigate the pollution characteristics and binding behavior of Hg in soils collected from the Chatian Hg mining deposit (CMD), southwestern China. The average concentration of Hg concentration in the CMD soils was 155 and 1,315 times higher than that in control soils and Chinese soils, respectively, suggesting that the CMD soils were heavily contaminated by the element. The finding was confirmed by Müller geoaccumulation index assessment with 75% very seriously polluted, 6.25% highly to very highly polluted and 18.75% moderately to highly polluted. Hg sources in the region were natural and anthropogenic: in addition to the pedogenic process and original geochemical situation, human mining-refining activities have also seriously impacted the redistribution of Hg in soils, especially in paddy soils. Based on the BCR protocol, soil Hg was divided into exchangeable (EXC), amorphous Fe-Mn oxides (AFe-MnOX), organic-crystalline iron oxides (OM-CFe) and residual (RES) fraction. The average percentage of the four fractions in the CMD followed the trend: RES (85.77%) > OM-CFe (12.44%) > AFe-MnOX (0.93%) ≥ EXC (0.86%), suggesting that the majority proportion of soil Hg in the study area remained of residual form inside the soil mineral matrix. However, their concentrations and percentages significantly varied among different locations and land use types. Soil physico-chemical parameters were key factors affecting the presence of Hg fraction. Generally, Hg fraction concentrations were positively correlated with the sand contents and soil pH values, which was presumably due to the basic anthropogenic input of Hg-containing materials and their similarity to sand in physical characteristics. However, organic matter caused adsorption-fixation and reduction-volatilization to coexist, which had opposite effects on Hg concentrations in soil, consequently exhibiting its dual nature.