Our proteomic and metabolic profile analysis of sweetpotato roots 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. Glucosinolate biosynthesis played a leading role in metabolic pathways of sweetpotao roots. More importantly, leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.