Chengkou County, located in the junction of Qinling geosyncline and Yangtze Plate, is chosen as a study area, 115 topsoil samples were collected, and soil pH, organic matter (SOM), major elements, total selenium (Se) in soil (Se_total) and phosphate extracted Se (Se_bioa) were determined. Results show that the concentration of Se_total is from 0.013 to 14.5 mg/kg with a median of 0.510 mg/kg, and the concentration of Se_total in 86.1% of samples is higher than 0.175 mg/kg, indicating a Se-enriched level. However, the median concentration of Se_bioais 0.046 mg/kg. Generally, the concentrations of Se_total and Se_bioa are the highest in the north region of Wuping Fault, and the concentrations of Se_total and Se_bioa are increased with the increase of the stratum age, indicating that the pedogenic rock controls the spatial distributions of Se_total and Se_bioa. This study proves the concentrations of Se_total and Se_bioa in topsoil varies greatly, even in the high geological background area, and the spatial difference is not only controlled by the pedogenic rock, but is also affected by other soil-forming factors.