Background: Understanding the mechanism of Hg accumulation in soil, which is a net Hg sink, at a national scale is important for protecting the environment and improving food safety. The mercury (Hg) distribution in surface soil in China is quite uneven, with relatively high concentrations in southeastern China and low concentrations in northwestern China. The reason for this distribution is inconclusive, especially at the continental scale. In this study, the relative contributions of the key impact factors, including dry and wet deposition, soil organic matter (SOM) and solar radiation to soil Hg, were evaluated. Results: Wet and dry deposition associated with precipitation and vegetation cover and emissions influenced by SOM are key factors controlling Hg distribution in surface soil. In southeastern China, high levels of wet deposition associated with the South Asia monsoon and dry deposition, enhanced by vegetation canopies, together with low levels of emissions caused by highly vegetated surfaces and solar radiation, are responsible for the high Hg levels in soil (> 0.08 mg/kg). In northeastern China, moderate levels of wet Hg deposition, high levels of dry deposition via throughfall and litterfall, low emissions due to weak solar radiation and high levels of SOM are responsible for high Hg accumulation in soil. In northwestern China, low levels of wet deposition, together with high emissions levels, low vegetation cover (bare soil) and SOM and strong solar radiation, contributed to the low Hg level in the surface soil (< 0.03 mg/kg). Conclusions: We suggest that wet deposition derived from the Asian monsoon, dry deposition linked to vegetated surfaces and Hg emissions associated with vegetation cover, SOM and solar radiation play key roles in the soil Hg level in China. In other terrestrial environments worldwide, especially in regions with significantly high levels of wet deposition and high amounts of vegetation cover and soil SOM, high Hg concentrations may exist in the surface soil.