The abundance and spatial distribution of mercury in soil samples covering nearly the whole of China (approximately 9 million km2) were obtained by the China Geochemical Baseline (CGB) project from 2008 to 2015. This project allows a further systematic study on national-scale Hg geochemical distribution patterns in soils. Comparing the data and maps, it was found that the Hg contents both in the top (0-25 cm) and deep soil (below 100 cm or C-horizon) of the karst area in southwestern China were relatively richer than that of any other geographical landscape areas. This regional-scale high Hg distribution is mainly due to high Hg geochemical background of bedrocks and soil formation on limestone. A large-scale epithermal metallogenic domain developed in southwestern China and the extensive distribution of Lower Cambrian black shale in southwest China lead to a high Hg geochemical background for parent rocks of soils. The chemical weathering of carbonate minerals and the geochemical behavior of Hg in the epigenetic environment result in Hg enrichment by ferric oxides, iron hydroxide and organic carbon in limestone soils. Human activities mostly result in local-scale Hg anomalies, but have little effect on this regional-scale anomaly.