<p><i>Curcuma wenyujin</i> is recognized as one of the traditional Chinese medicinal herbs classified under the ‘Eight Flavors of Zhejiang’. This herb is characterized by its high content of volatile oils and curcumin, with sesquiterpenes being the primary component. It exhibits a range of pharmacological activities, including anti-tumor, anti-inflammatory, and antiviral effects. The quality and yield of <i>C. wenyujin</i> are significantly influenced by abiotic stresses, with salt-alkali stress being one of the key factors among them. In this study, <i>C. wenyujin</i> was exposed to salt-alkali stress, with its leaves serving as the primary research object. Transcriptome and metabolome sequencing analyses were performed to explore the associated pathways and key genes in <i>C. wenyujin</i> that respond to salt-alkali stress. The results of transcriptome sequencing revealed a total of 438 differentially expressed genes significantly enriched in 12 pathways, including Biosynthesis of secondary metabolites, Metabolic pathways and Zeatin biosynthesis. Through comprehensive analysis, we have identified two key candidate genes, <i>CwPER5</i> and <i>CwBGLU32</i>, which are highly Likely to be involved in regulating metabolite synthesis under stress conditions. Additionally, non-targeted metabolomics sequencing identified a total of 781 metabolites, among which 166 were found to be significantly differentially accumulated. The most annotated metabolites were linked to the Biosynthesis of plant secondary metabolites pathway, followed by the ABC transporters pathway and the biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid pathway. This research offers a scientific foundation for the development and utilization of traditional Chinese medicine resources, specifically <i>C. wenyujin</i>, as well as a theoretical basis for breeding new varieties of <i>C. wenyujin</i> that exhibit resistance to salt-alkaline stress.</p>