High salt accumulation, resulting from the rampant use of chemical fertilizers in greenhouse cultivation, has deleterious effects on plant growth and crop yield. Herein, we delineated the effects of magnesium (Mg) oversupply on Perilla frutescens leaves, a traditional edible and medicinal herb used in East-Asian countries. Mg oversupply resulted in significantly higher chlorophyll content coupled with lower antioxidant activities and growth, suggesting a direct effect on subtle metabolomes. The relative abundance of bioactive phytochemicals, such as triterpenoids, flavonoids, and cinnamic acids, was lower in the Mg-oversupplied plants than in the control. Correlation analysis between plant phenotypes (plant height, total fresh weight of the shoot, leaf chlorophyll content, and leaf antioxidant content) and the altered metabolomes in P. frutescens leaves suggested an acclimatization mechanism to Mg oversupply. In conclusion, P. frutescens preferentially accumulated compatible solutes, i.e., carbohydrates and amino acids, to cope with higher environmental Mg levels, instead of employing secondary and antioxidative metabolism.