<p>Climate change, characterized by rising atmospheric CO₂ concentrations, is expected to significantly impact the growth, metabolism, and secondary metabolite production of medicinal plants. <i>Panax japonicus</i>, a rare and endangered medicinal herb of the Araliaceae (ginseng) family, is highly valued in traditional Chinese medicine for its bioactive saponins. This study investigated effects of elevated CO₂ (eCO₂) concentrations on the carbon and nitrogen metabolism of <i>P. japonicus</i>. <i>P. japonicus</i> rhizomes were cultivated in open-top chambers under three distinct atmospheric CO₂ regimes: ambient CO₂ (aCO₂), moderately elevated CO₂ (e1CO₂, 550 ± 10&#xa0;μmol&#xa0;mol⁻¹), and highly elevated CO₂ (e2CO₂, 750 ± 10&#xa0;μmol&#xa0;mol⁻¹), with exposure durations spanning short-term and prolonged periods. Under prolonged e1CO₂ conditions, activities of key enzymes involved in carbon metabolism and nitrogen metabolism were significantly higher than under aCO₂ conditions. However, under prolonged e2CO₂ conditions, only phosphate synthase (SPS) activity was significantly higher than under aCO₂, and nitrate reductase (NR) and glutamine synthetase (GS) activities were significantly lower (10.6% and 27.6%, respectively). The SPS/NR ratio of seedlings subjected to prolonged eCO₂ conditions was significantly higher than that of aCO₂-treated seedlings. Although prolonged e2CO₂ conditions were detrimental to nitrogen metabolism and to carbon and nitrogen metabolism balance, it was favourable to the content of saponins in the rhizomes of <i>P. japonicus</i>. Both the magnitude of CO₂ elevation and its application duration critically modulate <i>P. japonicus</i> responses in growth, carbon–nitrogen metabolism, and saponin production. This study contributing to the theoretical understanding of climate change impacts on medicinal plants.</p>