Selenium (Se) is a natural detoxifier of the heavy metal mercury (Hg), and the interaction between Se and Hg has been widely investigated. However, the ecological response of Hg to Se in Hg-contaminated farmland requires further study, especially the relationship between Se–Hg interactions and soil abiotic and biological properties. Through a field experiment, the effects of different levels of exogenous Se (0, 0.50, 0.75, 1.00, and 2.00 mg kg⁻¹) on Hg and Se transport in maize, soil properties, enzyme activities, and the microbial community in Hg-contaminated farmland were systematically studied. The Se treatments significantly reduced the Hg concentration in maize roots, stems, leaves, and grains and significantly increased the Se concentration in maize tissues. Except for the 0.75 mg kg⁻¹ Se treatment which significantly increased electrical conductivity compared to the control, other Se treatments had non-significant effect on soil physicochemical properties (pH, conductivity, organic matter content, and cation exchange capacity) and oxidoreductase activities (catalase, peroxidase, and ascorbate peroxide). The activities of soil invertase, urease, and alkaline phosphatase increased significantly after Se application, and the highest enzyme activities were observed with a 0.50 mg kg⁻¹ Se treatment. The bacteria and fungi with the highest relative abundance in this study were Proteobacteria (>30.5%) and Ascomycota (>73.4%). The results of a redundancy analysis and predictions of the microbial community showed that there was a significant correlation between the soil nutrient cycle enzyme activity, microbial community composition, and microbial community function. Overall, exogenous Se application was found to be a viable strategy for mitigating the impact of Hg stress on ecosystems. Furthermore, the results provide new insights into the potential for the large-scale application of Se in the remediation of Hg-contaminated farmland.