Low temperature stress during storage will greatly reduce the commodity value of sweetpotato. It is of great significance to study the molecular mechanism of cryopreservation tolerance and reduce the influence of low temperature in the storage process of sweetpotato. In this study, three sweetpotato varieties, ‘Shangshu 19’ (S19), ‘Yanshu 25’ (Y25) and ‘Sushu 16’ (S16), were stored at 9 ℃ and 6 ℃ for 35 days, respectively. Through comparative transcriptome analysis, we found that S19 had fewer differentially expressed genes after low temperature storage, while the opposite was observed for Y25, and S16 was intermediate. KEGG and GO analysis of differentially expressed genes showed that the expression level of proteasome related genes was higher in tuberous roots under low temperature stress. Finally, by comparing the transcriptome data of tuberous root of different varieties under different storage temperatures, a candidate gene Ibat.Brg.02F_G010830 that responds to low temperature stress during storage was obtained and it was annotated as cold-responsive protein kinase 1-like. qRT-PCR verified that the expression of this gene was consistent with the transcriptome data. The phylogenetic analysis of this gene and its alleles and orthologs was conducted, as well as the variation of this gene in different varieties. This study will provide support for the resolution of response mechanism under low temperature storage and the selection of varieties with low temperature storage tolerance.