Selenium (Se) serves as a natural detoxifier for the typical toxic heavy metal mercury (Hg), and the interactions between Se and Hg have attracted considerable scholarly attention in the field of Se and Hg. However, there is currently a lack of systematic summaries and discussions about Se–Hg interactions in soil–plant systems. This study summarizes the microscopic processes and macroscopic manifestations of Se–Hg interactions by exploring their characteristics, occurrence and mechanisms, revealing a dual-pump driving mechanism that emphasizes the “soil-root” and “atmosphere-leaf” interface of Se–Hg interactions in soil–plant systems. At the soil–root interface, HS⁻ (H₂S), Fe²⁺ and microorganisms are the key factors that cause the transformation of Se and Hg through oxidation, reduction, methylation and demethylation processes controlled by microbial or abiotic factors. Concurrently, Se reinforces the iron plaque barrier to decrease Hg absorption or to form HgSe complexes to limit Hg transportation into roots. Furthermore, the leaves, as the main plant tissue for Hg/Se uptake and bioaccumulation, are the key sites for the morphological transformation of Hg and Se, where Se–Hg interactions are likely to occur, and thus may constitute the other driving mechanism in the atmosphere–leaf interface. Finally, Se–Hg interactions are outlined after concluding the potential mechanisms, challenges and future research directions.