This study systematically investigated the regulatory mechanisms of precipitation changes on endogenous hormones, metabolome, and proteome of Vicia costata Ledeb., a key leguminous plant in desert steppe. Three precipitation treatments were established: 60% precipitation reduction (D), normal precipitation (CK), and 60% precipitation increase (W). Targeted plant hormone metabolomics, untargeted metabolomics, and proteomics technologies were employed to comprehensively analyze the response characteristics. The results showed that precipitation changes significantly affected the balance of endogenous hormones in Vicia costata. Six hormones, including ABA, ACC, cis-OPDA, cZR, tZ, and Typhasterol, exhibited significant differences among different treatments. A total of 1,058 metabolites were identified through metabolomics, with lipids and lipid-like molecules accounting for the highest proportion (30.34%). Differential metabolites were significantly enriched in pathways such as ABC transporters, phenylpropanoid biosynthesis, carbon fixation, and zeatin biosynthesis. Proteomic analysis revealed that the number of differential proteins was the highest in the D vs W comparison (41 proteins), which were significantly enriched in pathways including MAPK signaling pathway, starch and sucrose metabolism, and endoplasmic reticulum protein processing. Integrated analysis identified four common pathways (e.g., plant hormone signal transduction, starch and sucrose metabolism) that synergistically responded to water changes. This study uncovered the molecular adaptation mechanisms of Vicia costata to precipitation changes at the multi-omics level, providing a theoretical basis for the selection, breeding, and utilization of Vicia costata.