Here, a sucrose non-fermenting-1-related protein kinase alpha subunit (TaSnRK1alpha-1A) is identified as associated with cold stress through integration of genome-wide association study, bulked segregant RNA sequencing, and virus-induced gene silencing. It is confirmed that TaSnRK1alpha positively regulates cold tolerance by transgenes and ethyl methanesulfonate (EMS) mutants. A plastid-lipid-associated protein 6, chloroplastic-like (TaPAP6L-2B) strongly interacting with TaSnRK1alpha-1A is screened. Molecular chaperone DJ-1 family protein (TaDJ-1-7B) possibly bridged the interaction of TaSnRK1alpha-1A and TaPAP6L-2B. It is further revealed that TaSnRK1alpha-1A phosphorylated TaPAP6L-2B. Subsequently, a superior haplotype TaPAP6L-2B(30S) (/38S) is identified and confirmed that both R30S and G38S are important phosphorylation sites that influence TaPAP6L-2B in cold tolerance. Overexpression (OE) and EMS-mutant lines verified TaPAP6L positively modulating cold tolerance. Furthermore, transcriptome sequencing revealed that TaPAP6L-2B-OE lines significantly increased jasmonic acid (JA) content, possibly by improving precursor alpha-linolenic acid contributing to JA synthesis and by repressing JAR1 degrading JA. Exogenous JA significantly improved the cold tolerance of wheat plants. In summary, TaSnRK1alpha profoundly regulated cold stress, possibly through phosphorylating TaPAP6L to increase endogenous JA content of wheat plants.