Abstract: Drought conditions severely restrict plant growth and development, yet Ziziphus jujuba var. spinosa exhibits remarkable tolerance to such stress. To elucidate the molecular and metabolic processes underlying this tolerance, drought was imposed by withholding irrigation from seedlings for 28 days, followed by flavonoid profiling using liquid chromatography-mass spectrometry (LC-MS) and transcriptome analysis using RNA sequencing (RNA-seq). Drought stress induced substantial changes in flavonoid metabolism and markedly increased the accumulation of multiple flavonoid compounds. Transcriptomic profiling identified 26 316 high-quality unigenes, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that differentially expressed genes (DEGs) were significantly enriched in flavonoid biosynthesis, plant hormone signal transduction, and plant-pathogen interaction pathways. Integration of flavonoid and transcriptomic data further identified coordinated regulation of flavonoid biosynthesis during drought. In particular, the flavonoid biosynthetic genes CHS and CHI, encoding chalcone synthase and chalcone isomerase, respectively, were substantially upregulated under drought stress, and their expression patterns were strongly correlated with flavonoid accumulation. Collectively, these results indicate that drought induces coordinated activation of key flavonoid biosynthetic genes in Z. jujuba var. spinosa, promoting flavonoid accumulation during water deficit. The identified drought-responsive genes provide candidate targets for genetic improvement and a molecular basis for breeding drought-tolerant germplasm.