Selenium (Se) is an essential micronutrient for humans given its varying health benefits. It is generally recognized that China has a wide belt of low-Se soil stretching from the northeast to southwest. Nevertheless, there are Se-enriched areas distributed in the low-Se belt of China. However, the quantificational relationships among soil properties, topographic characteristics, parent materials, land use and soil Se content in those Se-enriched soils remain to be elucidated. Similarly, the key driving factors of the Se-enriched soil in the low-Se geological belt need to be documented. These aims could be an useful basis for evaluating the health of the soil ecosystem (in terms of Se toxicity or deficiency) and the potential intake of Se by humans from soils to food crops and animal products. To solve the above questions, Jiangjin district, Chongqing City, as an area in low Se red beds, was selected, and 156 topsoil samples were collected to explore the relationships between Se content in topsoil under various land use type and soil properties (pH, organic matter (OM), major elements content in topsoil) and topographic characteristics such as elevation (H), slope (SL), and topographic wetness index (TWI) and geological condition (stratum). Geostatistics, principal component analysis (PCA) and Geodetector were used to analyze the controlling factors of Se distribution in topsoil. The results show that in the analyzed topsoil (1) Se contents vary from 0.039 to 1.110 mg/kg, with a mean of 0.315 mg/kg, and higher than the background value of Chinese soil (0.290 mg/kg). 82.3% are classified as having moderate Se levels (Se > 0.175 mg/kg). (2) The Se contents in northeast of Jiangjin district are higher (Se > 0.315 mg/kg) than the midwest (Se < 0.315 mg/kg). (3) The key controlling factor of the soil Se distribution is OM. In addition, the soil weathering and leaching process and pedogenic rock are the secondary factors controlling Se distribution. Together, these findings reveal that Se-rich soil of low Se belt tends to be distributed in regions with higher OM, stronger leaching, and carbonate parent materials. These observations are beneficial to explore the Se-rich soil resources in low Se region in China.