Cold stress adversely affects plant growth and development, and crop productivity and quality. The transcription factor CBF-dependent cold signaling pathway plays a key role in cold acclimation in Arabidopsis; however, the protein kinases involved in this pathway remain unknown. Here, we identified three kinds of protein kinases regulating this signaling pathway. OST1/SnRK2.6 (Open Stomata 1), a protein kinase involved in ABA signaling, is activated by cold stress, in a process governed by the protein phosphatase EGR2 (Clade E Growth Regulating 2). OST1 interacts with and phosphorylates ICE1 and BTF3 (a subunit of the nascent polypeptide-associated complex), to positively regulate CBFs and plant freezing tolerance. We also found that OST1 phosphorylates two U-box E3 ligases to enhance their E3 activity, which in turn targets the degradation of MYB15, a negative regulator of cold signaling pathway under cold stress. To avoid the excess cold response, MPK3/MPK6 are activated, which phosphorylate and destabilize ICE1 to negatively regulate CBF expression and freezing tolerance. Moreover, cold also activates a plasma membrane-localized kinase CRPK1 (Cold-Responsive Protein Kinase 1), which phosphorylates 14-3-3 proteins and mediates their import from the cytosol to the nucleus to induce CBF protein degradation, thus fine-tuning CBF cold signaling. Our data thus suggest that phosphorylation plays a pivotal role in regulating CBF-dependent cold signaling in Arabidopsis.