In Jiangxi Province, Fengcheng City is a typical area rich in soil selenium. Based on the data of the 699 soil samples collected from the surface layer (0-20 cm) of farmlands in Fengcheng City in 2015—2016, geostatistical analysis, correlation analysis and geographic detectors were applied to systematically analyze spatial differentiation of soil selenium in distribution and its influencing factors. The research was done in an attempt to provide certain valuable reference for conservation of soil selenium and the production function of the selenium-rich land. Results show that soil selenium contents of Fengcheng City ranged from 0.13 to 0.69 mg∙kg^-1 with coefficient of variation being 27.27% or moderate in level and averaged 0.33 mg∙kg^-1, about 1.14 times as high as the soil selenium background value (0.29 mg∙kg^-1) of the country. Semi-variogram function analysis shows that the range of soil selenium was 12.86 km and quite large for spatial autocorrelation, and that its nugget effect value was 44.30%, which indicates that spatial variation of soil selenium was mainly affected by structural factors. In the spatial distribution, hot spot areas (area where high values concentrate) were distributed mainly in the west of Quangang Town, the southeast of Dongjia Town, the center of the Shangzhuang Neighborhood, the southwest of Shangtang Town, the northwest of Qujiang Town, the center and south of Luoshi Town and the southwest of Xiushi Town. Arsenic, copper, mercury, potassium oxide, calcium oxide, pH, soil parent material and elevation are factors affecting spatial variability of the soil selenium but vary in extent (P <0.05). Arsenic is the highest in the effect, explaining 29% of the variability, and plays an important role in the enrichment and migration of selenium in the topsoil of Fengcheng City.