Background <p>A major public health concern is the increasing incidence of circadian syndrome (CircS), especially in older people. While physical activity (PA) is recognized for its metabolic benefits, its longitudinal association with CircS, especially in the Chinese context, remains to be fully elucidated. This research sought to investigate this relationship using a national longitudinal cohort.</p> Methods <p>This prospective study utilized data from the China Health and Retirement Longitudinal Study (CHARLS) 2011–2015, including 4,045 participants aged above 45. Participants were categorized as sedentary (PA-), or into low, moderate, and high activity groups based on tertiles. Cox proportional hazards models were established to estimate association between PA and CircS, with adjustments for covariates. Cumulative incidence curves were plotted via the Kaplan-Meier (KM) method. The dose-response relationship was examined with restricted cubic splines (RCS), and subgroup analyses were implemented via stratified Cox regression.</p> Results <p>Among the included population (CircS: <i>n</i> = 694), a significant, inverse dose-response association was observed between PA levels and the risk of CircS. Compared to the sedentary group, the moderate and the high PA groups were both notably associated with reduced risk of CircS, as reflected by hazard ratios less than 1. KM analysis showed a clear gradient of decreasing CircS incidence with increasing levels of PA. RCS analysis confirmed a linear inverse association. Subgroup analysis showed that the inverse association was consistent across populations defined by aged less than 60 years, male, and other characteristics.</p> Conclusion <p>Higher PA levels are linked to a lower risk of developing CircS in middle-aged and older Chinese adults, supporting the potential role of PA in the primary prevention of CircS.</p> Trial registration <p>Not applicable.</p>