Circadian disruption affects various physiological processes, including male fertility. However, the effects and mechanism of circadian disruption on sperm DNA fragmentation (SDF) remain largely unexplored. In this study, we investigated this relationship using a mouse model of circadian disruption to assess in vivo effects, human sperm samples to evaluate clinical associations, and GC2 spermatocyte cells for mechanistic insights. A model of circadian disruption was established using C57BL/6 J male mice subjected to a weekly 12-h inversion of the light-dark cycle for 8 weeks, which resulted in significant sperm DNA damage in mice. Analysis of differentially expressed genes from RNA sequencing of testes from circadian-disrupted mice revealed that the homologous recombination (HR) repair pathway was significantly affected. Potential correlations between CREB1 expression and SDF were explored in human sperm (n = 40). CREB1 mRNA expression detected using droplet digital PCR was lower in patients with high sperm DNA damage than in the control group. In GC2 germ cells, Creb1 knockdown reduced cell proliferation and increased sensitivity to oxidative stress; moreover, it increased double-strand breaks and decreased protein levels of the DNA repair genes BRCA1, MRE11, and RAD51. Luciferase reporter and ChIP assay confirmed the transcriptional regulation of CREB1 on BRCA1 expression. Overall, circadian disruption suppressed CREB1 expression, which contributed to deficient HR repair and ultimately led to SDF. CREB1 expression was associated with sperm DNA damage in human. Our findings may have implications for understanding male health under circadian disruption and could provide novel avenues for therapeutic strategies to address SDF.