BackgroundIt was reported that metabolic syndrome increases the risk for cognitive impairment and circadian rhythm may influence cognition behavior. Identifying the potential risk factors is essential to screen individuals with neuronal dysfunction, neuronal loss, and cognitive decline and prevent cognitive impairment and dementia development.MethodsWe clarified participants by the presence of metabolic syndrome (MetS) and circadian syndrome (CircS) and employed three multivariable Generalized Estimating Equation (GEE) models to control the potential confounding factors and estimate the β values for cognitive function using as referents those had neither MetS nor CircS at baseline. The cognitive function consists of episodic memory and executive function was estimated via the modified Telephone Interview for Cognitive Status (TICS) every two years until 2015.ResultsThe mean age of the participants was 58.80 (8.93) years and 49.92% (male). The prevalence of MetS and CircS was 42.98% and 36.43%, respectively. 1,075 (11.00%) and 435 (4.45%) participants had either MetS or CircS alone and 3,124 (31.98%) had both CircS and MetS. Participants with both MetS and CircS compared with normal had a significantly decreased cognitive function score during the 4-years cohort (β = -0.32, 95% CI: -0.63, -0.01) with the complete model, as well as among participants who suffered from CircS alone (β = -0.82, 95% CI: -1.47, -0.16), while not among participants with MetS alone (β = 0.13, 95% CI: -0.27, 0.53). Specifically, compared with the normal population a significantly lower score was discovered in the episodic memory (β = -0.51, 95% CI: -0.95, -0.07), while slightly lower in executive function (β = -0.33, 95% CI: -0.68, -0.01) among individuals with CircS alone.ConclusionsIndividuals with CircS alone or both MetS and CircS have a high risk of cognitive impairment. The association was even stronger in participants with CircS alone than those with both MetS and CircS, suggesting CircS probably have a stronger association with cognitive functioning than MetS and could be a better predictor for cognitive impairment.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12877-023-03996-x.