Objective: To explore the regulatory effects of circadian rhythm disruption on circadian clock genes in the hypothalamus and amygdala at different time points in insomnia model mice based on Ying-Wei theory. Methods: 104 8-week-old female ICR mice were randomly divided into a normal group (n=52) and a model group (n=52), each further subdivided into subgroups at 6:00, 12:00, 18:00, and 24:00 (13 mice per time point). The model group received intraperitoneal injections of PCPA for 3 days, while the normal group received equivalent volumes of saline. Behavioral tests were conducted to evaluate sleep latency, total sleep duration, and anxiety-depression-like behaviors. Immunofluorescence staining was used to observe nuclear translocation of Period Circadian Regulator 1 (PER1) and Cryptochrome Circadian Regulator 1 (CRY1) in the hypothalamus and amygdala. RT-qPCR and Western blot were performed to measure mRNA and protein expression levels of circadian clock genes. Results: Compared with the normal group, the model group exhibited prolonged sleep latency, reduced sleep duration (P<0.01), decreased sucrose preference (P<0.01), increased grooming frequency, and extended central exploration distance in the open field test (P<0.01). Significant differences in mRNA and protein expression of core clock genes (PER1, CRY1, CLOCK, and BMAL1) were observed between the two groups at all time points, with inconsistent expression patterns between the hypothalamus and amygdala. In the model group, the peak nuclear co-localization of PER1 and CRY1 in the hypothalamus was advanced by 4–6 hours, while their nuclear co-localization peaks in the amygdala were phase-shifted by approximately 12 hours compared to the normal group. Conclusion: Dysregulated expression of core circadian clock genes in insomnia mice is associated with Ying-Wei imbalance-induced circadian rhythm disruption. The mechanism may involve differential nuclear dimerization of PER1 and CRY1 across brain regions.