Selenium (Se) is an essential trace element for humans. In order to investigate how soil Se is influenced by topography and soil properties, we selected Yongjia County, an area with mountainous topography, as a study area. This study used cultivated soil data to comprehensively analyze the effects of topography and soil properties on Se mobility and bioavailability and to identify the key factors influencing Se distribution in the environment. Factors considered in this study were elevation, slope, topographic wetness index, the coefficient of weathering and eluviation, pH, organic matter, and Fe₂O₃. The concentration of total soil Se (0.382 ± 0.123 mg kg⁻¹) was far higher than the background value of soil in China, and 98% of the soil samples were classified as having moderate Se levels (>0.175 mg kg⁻¹), indicating Yongjia County is a Se-rich region in China. Phosphate extracted Se accounted for an average of 9% of the total Se and was significantly associated with soil total Se, Fe₂O₃, pH, and the coefficient of weathering and eluviation. Fe₂O₃ primarily controlled Se adsorption, fixation, and availability in soil. Under the geo-environmental conditions in the study area, the total Se in the soil increased first and then decreased with increases in elevation, slope, and the topographic wetness index, and the phosphate extracted Se showed similar patterns except for the elevation. The findings showed that topographical attributes and soil physicochemical properties synthetically influenced the distribution and bioavailability of Se in soil.