Abstract Objective To explore the association between circadian syndrome (CircS) and the prevalence of kidney stones in overweight people. Materials and methods A cross-sectional analysis was conducted based on the NHANES 2007–2018. Overweight people aged ≥ 20 years were the target population. Three multivariable logistic regression models were built to examine the association between CircS and kidney stones. Subgroup analysis based on age, gender, and race were also employed. Interaction and stratification analysis was also conducted to identify whether some factors modify the association. Result A total of 4,603 overweight participants were included in the study. The multivariable logistic regression suggested that CircS was positively associated with the prevalence of kidney stones (OR = 1.422, 95% CI 1.057 to 1.912). The subgroup analysis showed that the association was more obvious in females (OR = 1.604, 95% CI 1.023 to 2.516) or in the population aged 35 to 49 years old (OR = 2.739, 95% CI 1.428 to 5.254). Additionally, the same trend was present when people were Mexican American (OR = 3.834, 95% CI 1.790 to 8.215) or other races (OR = 4.925, 95% CI 1.776 to 13.656). The interaction and stratification analysis showed that the results above were robust. Conclusion CircS was positively associated with the prevalence of kidney stones in overweight people, especially people as females, aged 35 to 49, and Mexican Americans.