Soil selenium (Se) is seriously deficient in Congqing of southwest China. A Multi-Purpose Regional Geochemical Survey (MPRGS) was performed in the Three Gorges Reservoir Region (Chongqing Section) in order to stimulate the development of native Se-rich agricultural resources. Soil were collected with the sampling density of 1 sample/4 km² for surface soil and 1 sample/16 km² for deep soil, respectively, and then the spatial distribution of soil Se and its influential factors were studied. The results showed that the content of Se in surface soil ranged from 0.006 to 5.79 mg/kg with a mean of 0.16 mg/kg, for the total region, about 39.25% and 33.94% were Se deficient and potentially deficient, 25.77% was sufficient, while only 0.16% is rich and poisoning. Se in deep soil ranged from 0.03 to 0.62 mg/kg with a mean of 0.12 mg/kg, and Se deficient and potential deficient accounted for 67.36% and 20.68% in area, respectively. Se content in surface soil varied significantly with soil type, with highest in yellow soil, followed by limestone soil, which were significantly higher than those in paddy soil and purple soil. There were no significant differences in Se contents among different land use types, but Se contents were higher in forestry and construction land types. The obviously Se enrichment in surface soil was found, which accounted to 76.97% of the total area but 56.93% of which was weak enrichment. Se content in surface soil was significantly positively correlated with soil organic matter and total nitrogen contents, altitudes and slope, but significantly negatively correlated with soil pH. The associated relationship was observed between Se and heavy metal contents (As, Cd, Cr, Cu, Hg, Ni, Zn and Pb) in surface soil, particularly of Cd. Furthermore, Fe and Al contents were also important influential factors of Se content in surface soils.