The circadian clock is a timekeeping mechanism synchronizing self-sustained physiological rhythms to the 24-h environmental cycles. We used the split luciferase complementation assay (LCI) to study dynamic protein-protein interactions (PPIs), and engineered full-length clock genes fusion constructs carrying cLUC or nLUC. We found the detached shoot and root possess 24-h rhythmic PPIs between clock core components, in which circadian periodicity exhibits a difference in organs. Compared to wild-type, the period length difference between shoot and root was not remarkable in prr7-3 and prr7-3 prr9-1 mutants. Further, the phase transition curve (PTC) indicated that shoot and root clock respond differently to the resetting cues of ambient temperature. PRR9 and PRR7 compensate circadian period between 22°C and 28°C in shoot, not in root. In addition, we found that a subfamily of zinc finger transcription factors, B-box (BBX)-containing proteins, have a critical role in fine-tuning circadian rhythm. Overexpressing Arabidopsis thaliana BBX19 and BBX18 significantly lengthened the circadian period, and the null mutation of BBX19 accelerated the clock pace. Moreover, BBX19 and BBX18 protein, which are expressed during the day, physically and dynamically interacted with PRR9, PRR7, and PRR5 in the nucleus in precise temporal ordering from dawn to dusk, consistent with the respective protein accumulation pattern of PRRs. Collectively, our findings demonstrate the circadian rhythmicity and tissue specificity of interactions between clock proteins, which determine the regulation of their target genes to perform physiological functions and stress responses at specific times of a day and specific organs.