Silicon (Si) and selenium (Se) have been recognized as beneficial elements for plant tolerance to abiotic stresses. However, the mechanisms responsible for the alleviating effects of Si-Se interactions on salt stress are still not clear. In this study, we compared the effects of Si and Se alone and in combination on the growth, sodium (Na) accumulation, photochemical parameters, the net Na+ flux and expression of salt resistance-related genes in maize plants under salt stress. The results showed that the addition of Si and Se significantly mitigated salt toxicity, and an obvious synergistic interaction was found between them. The application of Si and Se protected the structure and function of the photosynthetic apparatus from salt stress, and no differences were found between single and combined treatments. The combination of Si and Se significantly increased the net Na+ efflux and resulted in decreased Na+ influx in the root meristematic zone. Furthermore, salt stress-responsive genes, including ZmNHX and ZmSOS2, were upregulated under the combined treatment of Si and Se. These results indicate that the synergistic effects of Si and Se against salt stress were caused by the upregulated expression of transporter genes involved in Na+ uptake, exclusion and sequestration into vacuoles in roots.