Background: Sweetpotato (Ipomoea batatasL.) is one of the seven major food crops grown worldwide. Cold stress often can cause protein expression pattern and substance contents variations for tuberous roots of sweetpotato during low-temperature storage. Recently, we developed proteometabolic profiles of the fresh sweetpotatoes (cv. Xinxiang) in an attempt to discern the cold stress-responsive mechanism of tuberous root crops during post-harvest storage.Results: For roots stored under 4 °C condition, the CI index, REC and MDA content in roots were significantly higher than them at control temperature (13 °C). The activities of SOD, CAT, APX, O₂^.-producing rate, proline and especially soluble sugar contents were also significantly increased. Most of the differentially expressed proteins (DEPs) were implicated in pathways related to metabolic pathway, especially phenylpropanoids and followed by starch and sucrose metabolism. L-ascorbate peroxidase 3 and catalase were down-regulated during low temperature storage. α-amylase, sucrose synthase and fructokinase were significantly up-regulated in starch and sucrose metabolism, while β-glucosidase, glucose-1-phosphate adenylyl-transferase and starch synthase were opposite. Furthermore, metabolome profiling revealed that glucosinolate biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis as well as protein digestion and absorption played a leading role in metabolic pathways of roots. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.Conclusions: Our proteomic and metabolic profile analysis of sweetpotatoes stored at low temperature reveal that the antioxidant enzymes activities, proline and especially soluble sugar content were significantly increased. Most of the DEPs were implicated in phenylpropanoids and followed by starch and sucrose metabolism. The discrepancy between proteomic (L-ascorbate peroxidase 3 and catalase) and biochemical (CAT/APX activity) data may be explained by higher H₂O₂levels and increased ascorbate redox states, which enhanced the CAT/APX activity indirectly. Glucosinolate biosynthesis played a leading role in metabolic pathways. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.