Cyclocarya paliurus (Batalin) Iljinskaja is a rare, endemic tree species in China. The leaves of C. paliurus contain a high concentration of biologically active compounds, and they are often used to make herbal tea. Exogenous selenium (Se) enrichment can promote the levels of active ingredients in C. paliurus. To explore the effects of exogenous Se enrichment, this study applied different concentrations of sodium selenite solution on the leaves (0, 40, 80, 120, 160, and 300 mg/L) and measured the changes in Se, secondary metabolites, soluble sugar, soluble protein, starch, and trace elements in the leaves at different treatment times. The results showed that with the increase in the concentration of sodium selenite spray, the selenium content in the leaves of C. paliurus gradually increased, and high selenium concentrations could cause seedling burning to the leaf surface (>160 mg/kg). When the selenium treatment concentration was 80 mg/kg, the selenium content reached the maximum value of the selenium-rich tea standard (4 mg/kg). The content of polyphenols and most elements reached their maxima under the treatment of 40 mg/L Na2SeO3, except for Mg and Mn, which peaked at 300 mg/L. The content of soluble sugars (38.1 mg/g) and starch reached their maxima under relatively high selenium treatment concentrations, whereas soluble protein (10.63 mg/g) exhibited its maximum value in the control group. The optimal harvest time was mainly concentrated in the 10–20 day treatment period. The objective of this research is to investigate the effects of exogenous selenium application on the nutritional quality of C. paliurus leaves. The findings will provide guidance for the effective cultivation of selenium-enriched Poria cocos as a medicinal and health-promoting product.