Curcuma wenyujin, a perennial herb of the ginger family, is renowned for its significant medicinal properties. Phosphorus (P), a vital nutrient for plant growth and development, has seen its levels, particularly organic P, increase in the soils of agricultural regions in southern China, presenting new challenges for nutrient management. This study aimed to uncover the molecular responses of C. wenyujin seedlings to both normal and high phosphorus (HP) conditions, shedding light on their adaptation strategies to P stress. Through transcriptome and metabolome analyses of the seedlings under normal and HP conditions, we identified 1,793 metabolites, with 195 showing differential expression. Notably, KEGG enrichment analysis highlighted 35 significantly differential accumulation metabolites (DAMs). Comparing the control group (CK) and HP treated groups (T) revealed 840 differentially expressed genes (DEGs), pinpointing the molecular divergences in response to varying P levels. Importantly, we found a potential gene, purple acid phosphatase 17 (pap17) that may cofer HP stress conditions in C. wenyujin. That elucidated the response variations of C. wenyujin seedlings to diverse P concentrations. The research suggested that C. wenyujin may adjust to varying P levels by modulating metabolites and genes linked to amino acid and phenylpropane metabolism. It highlighted the sophisticated mechanisms plants utilize to manage P stress, offering insights into their survival tactics in settings where P availability changes.