Selenium (Se) is regarded as an essential trace element for the human body, and diet has been recognized as the most economical, safe and effective way for humans to obtain selenium. By systematically sorting out the research status of selenium fortification in soil-crop systems at home and abroad, the migration and transformation mechanism of selenium in soil-crop systems, the main fortification technology approaches and the health effects of selenium fortification were summarized and discussed. It is indicated that soil-crop system selenium fortification has become a current research hotspot in the global agricultural and nutritional fields, and China has been the main contributing country in this field. The speciation and bioavailability of soil selenium, as well as its absorption and translocation in crops, are affected by soil parent material, soil physical and chemical properties and microbial activities. Selenium in different forms is absorbed by crop roots and leaves, and subsequently accumulated in crops through specific transport mechanisms. The total content and speciation of selenium in the edible parts of crops can be optimized through selenium fortification technologies such as agronomic regulation, genetic improvement and microbial-assisted fortification. The health effects of selenium-fortified crops are jointly affected by selenium content, speciation, bioaccessibility, soil environmental conditions, rhizosphere microorganisms, fortification methods, crop varieties and cooking procedures, with the nutritional benefits of selenium ultimately regulated accordingly. Further attention should be focused on the mechanism of selenium speciation transformation, as well as the improvement of stability and regional adaptability of selenium fortification technologies. Thus, the large-scale and safe application of relevant technologies can be advanced, offering scientific support for improving selenium nutrient utilization efficiency, optimizing population selenium nutritional status and protecting public health.