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Selenium (Se)-rich <i>Cyclocarya paliurus</i> is popular for its bioactive components, and exogenous Se fortification is the most effective means of enrichment. However, the effects of exogenous Se fortification on the nutritional quality of <i>C. paliurus</i> are not well known. To investigate the nutrient contents and antioxidant properties of <i>C. paliurus</i> following Se treatment, we used a foliar spray to apply Se in two forms—chemical nano-Se (Che-SeNPs) and sodium selenite (Na₂SeO₃). Sampling began 10 days after spraying and was conducted every 5 days until day 30. The Se, secondary metabolite, malondialdehyde contents, antioxidant enzyme activity, Se speciation, and Se-metabolism-related gene expression patterns were analyzed in the collected samples. Exogenous Se enhancement effectively increased the Se content of leaves, reaching a maximum on days 10 and 15 of sampling, while the contents of flavonoids, triterpenes, and polyphenols increased significantly during the same period. In addition, the application of Se significantly enhanced total antioxidant activity, especially the activity of the antioxidant enzyme peroxidase. Furthermore, a positive correlation between the alleviation of lipid peroxidation and Se content was observed, while methylselenocysteine formation was an effective means of alleviating Se stress. Finally, Na₂SeO₃ exhibited better absorption and conversion efficiency than Che-SeNPs in <i>C. paliurus</i>.