In order to study the distribution of selenium in surface soil and its main influencing factor, we collected 360 surface soil samples and four groups of soil profiles with 210 corresponding parent rock samples in Langao County, Shaanxi Province (a typical high-selenium area of Daba Mountain). Samples were analyzed for trace elements by using ICP-MS, ICP-OES and HG-AFS. The results show the following. (1) selenium content in surface soils of Langao County varies greatly (0.03–16.96 mg/kg). The mean selenium content in surface soils of Langao County is 0.99 mg/kg, higher than the global (0.4 mg/kg) and China (0.29 mg/kg) soil average, and 3.4 times the mean of soil selenium in China. (2) Selenium content of bedrock in Langao County also varies greatly (0.01–56.22 mg/kg), with an average selenium content of 2.02 mg/kg, which is 40 times higher than the upper crust (0.05 mg/kg). (3) Selenium content in the strata of the Late Precambrian–Early Paleozoic and its variation is an important factor affecting the spatial variation of soil selenium content. The black rock series (carbonaceous slate and silicon-bearing carbonaceous slate) of the Upper Ediacaran–Cambrian on the north side has the highest mean selenium content (> 7.92 mg/kg), and the selenium content of the surface soil in the distribution area can reach up to 16.96 mg/kg. The Middle Cambrian, Upper Cambrian, Ordovician and Silurian (limestone and marl) in the south has the lowest mean selenium content (< 2 mg/kg), and the selenium content of surface soil in the distribution area is lower than 0.8 mg/kg mostly. (4) Soil samples at different depths in the same soil profile have similar composition of rare earth elements (REE), and bedrock and corresponding topsoil has similar composition of REE. This study indicates the selenium content in the topsoil varies greatly, even in high-selenium area. And the difference of selenium distribution is closely related to the original selenium content of the bedrock.