Cyanobacteria are the simplest organisms with a confirmed circadian clock system. The pacemaker of cyanobacterial circadian clock is made of three proteins, KaiA, KaiB, and KaiC. A major finding on this system is that the circadian oscillation of the pacemaker system is independent of transcriptional/translational controls, and what is more intriguing is that this oscillation can be reconstituted in vitro with only these three proteins, in addition to ATP and an appropriate inorganic buffer. Molecular studies have shown that KaiA promotes the self-phosphorylation of KaiC, whereas KaiB antagonize KaiA's role and induce the de-phosphorylation of KaiC. An unsolved question is how KaiB interacts with KaiC exactly, including the binding site of KaiB on KaiC, the oligomerization form of KaiB, and the exact modulating mechanism of KaiB. Here, we reviewed the most recent progress on the KaiB-KaiC interaction mechanism, including our preliminary results on the KaiB-KaiC interaction, and provided a possible molecular mechanism of the molecular oscillator. We hope this review will provide a timely perspective on the study of this model system.