<p>Expanding the cultivation range of <i>Daodi</i> medicinal materials is crucial for mitigating the shortage of high-quality medicinal resources. <i>Cynanchum auriculatum</i>, a salt- and alkali-tolerant medicinal plant, faces significant cultivation challenges due to soil salinity and alkalinity. This study systematically investigates the physiological, transcriptional, and metabolic responses of <i>C</i>. <i>auriculatum</i> under varying saline and alkaline conditions. We established the species-specific tolerance thresholds at soil salt content &lt; 3.38‰ and pH &lt; 8.16, based on a 50% reduction in fresh weight. Beyond these thresholds, leaf structure and photosynthetic capacity were significantly impaired, with salt exhibiting more severe effects than alkaline conditions. Notably, high salinity essentially enhanced antioxidant enzyme activity, whereas alkaline conditions exacerbated damage. Under supra-threshold conditions, the number of differential metabolites increased, primarily enriched pathways related to phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis. Transcriptomic analysis further revealed that saline and alkaline stress upregulate key genes, including 4CL, COMT, and F5H, leading to elevated levels of critical metabolites such as phenylalanine, caffeic acid, ferulic acid, and sinapic acid, thereby enhancing stress tolerance. Importantly, within the identified threshold range, <i>C</i>. <i>auriculatum</i> maintained stable yields, with an increase in differential metabolites. However, exceeding the threshold resulted in a decline in both the number of differential metabolites and overall production. This study provides valuable insights into optimizing the cultivation of <i>C</i>. <i>auriculatum</i> and enhancing its stress tolerance.</p> Graphical abstract <p></p>