Selenium (Se) is an essential micronutrient for many organisms (including soil microorganisms, plants, animals, and humans), and has dual biological effects on plants, animals, and humans. The migration, transformation, and enrichment of Se in soil-plant systems have attracted considerable attention for more than half a century. There are five forms of soil Se: soluble Se (SOL-Se), exchangeable carbonate-bound Se (EXC-Se), iron-manganese oxide-bound Se (FMO-Se), organic matter-bound Se (OM-Se), and residual Se (RES-Se), of which SOL-Se and EXC-Se are characterized by bioavailability. OM-Se can be converted into soluble Se by the decomposition of organic matter and is a potentially effective selenium source in soil. The Se content of different plants depends on the soil-available Se content and the Se absorption and enrichment levels of different plants. Therefore, the bioavailability of soil Se plays a critical role in determining the Se content in the food chain, and soil-available Se can improve plant stress resistance by regulating the rhizosphere environment and metabolic processes. Soil-plant system Se migration is a complex biogeochemical process that is dominated by coupled crustal movement, parent rock properties, climate, geomorphology, soil environment (physico-chemical properties and microbial activity) conditions, soil Se content and chemical properties, plant species and biological habits, and field management processes. For the rational utilization of soil Se resources, research needs to focus on Se migration, transformation, and enrichment in plants, especially the main food crops, vegetables, fruit trees, and Authentic Chinese herbs. This study provides basic data for Se biofortification in Se-deficient areas, and crop selection, food selection, and risk assessment in Se-rich areas.