Maize (Zea mays L.) is a cold-susceptible species that often faces cold stress, which has an adverse impact on growth, development, and yield in maize. We identified several genes that play important roles in regulating cold tolerance in maize using multiple approaches. Using reverse genetics approach, we identified type-A Response Regulator 1 (ZmRR1) and ZmbZIP68 as positive and negative regulators of maize tolerance, respectively. Their protein stabilities were controlled by ZmMPK8-mediated phosphorylation. ZmRR1 has natural variations in its coding region, results in the divergence of protein stability and thus chilling tolerance among maize inbred lines. The ZmbZIP68 locus was a target of selection during early domestication. Moreover, using metabolite genome-wide association study (mGWAS), the natural variation in the ZmICE1 promoter was identified to modulate the amino acid homeostasis and cold tolerance in maize inbred lines. Finally, we identified a new regulator regulating maize cold tolerance by forward genetic approach, and the detailed regulatory mechanism will be presented.