BACKGROUND: Common bean (Phaseolus vulgaris L.) is a thermophilic crop, and exposure to cold stress can significantly impact their yield and quality. To elucidate the impact of cold stress on cold-tolerant 'Wei Yuan' (WY) and cold-sensitive 'Bai Bu Lao' (BBL) of common bean, the mechanism of cold tolerance was studied by physiological and biochemical and multi-omics analysis. RESULTS: In this study, lower relative conductivity and higher malondialdehyde content after cold stress endowed 'WY' seedlings with cold tolerance. A total of 11,837 differentially expressed genes (DEGs) and 923 differential metabolites (DEMs) were identified by transcriptome and metabolomics analysis. Joint analysis showed that under cold stress, DEGs and DEMs in common beans are extensively engaged in sugar, amino acid and isoflavonoid biosynthesis, flavone and flavonol biosynthesis, and plant hormone signal translation, especially related to isoflavone biosynthesis. In addition, it was also found that bHLH and MYB family transcription factors may be involved in the cold signal transduction of common bean. CONCLUSIONS: The above results will provide a theoretical basis for the cold tolerance mechanism of common beans and provide help for the screening of cold-tolerant resources of common beans. CLINICAL TRIAL NUMBER: Not applicable.