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Selenium (Se) is an essential element for humans, playing a critical role in the functioning of the immune system. The global prevalence of dietary Se deficiency is a significant public health concern, largely attributed to the low levels of Se present in crops. The sufficient Se in plants and humans is determined by the presence of stable Se sources in the soil. The Leizhou Peninsula is an important agricultural region in China, but the concentration and spatial distribution of Se in its soils remain unclear. To address this issue, we analyzed Se concentration data from 3333 soil samples collected at the depth of 0–20 cm from the Leizhou Peninsula, covering an area of 13,225 km2. The results indicate that the mean soil Se concentration was 0.50 mg kg−1, with Se-enriched soils being widely distributed. This provides prospects for the development of Se-enriched crops. Using random forest (RF) modeling and correlation analysis, the clay minerals (Fe–Al oxides), chemical index of alteration (CIA), and soil organic carbon (SOC) have been identified as the principal determinants of Se distribution in soil. During the weathering processes of the basalts, Fe–Al oxides serve as a crucial factor in Se accumulation in the red soils. Furthermore, the tropical climate further contributes to increasing the degree of weathering and the proportion of clay minerals and SOC in the soil. Atmospheric deposition derived from marine and precipitation is another important factor that promotes Se flux into soils. In conclusion, the distribution pattern of Se is jointly determined by the weathering process of basalt and climatic conditions. The results of the geographically weighted regression (GWR) analysis revealed that SOC, Al2O3, TFe2O3 and CIA change spatially and exhibit a spatial non-stationarity relationship with Se. This study offers a theoretical foundation and practical guidance for the sustainable development of Se-enriched agriculture and similar climate settings worldwide. [ABSTRACT FROM AUTHOR]