This study aimed to examine the association between habitual types of sleep initiation time and metabolic syndrome. A total of 2674 participants aged 40 to 69 years (48.73% men, mean age 48.33 ± 7.18 years), who were free of cardiovascular disease or cancer and were not shift workers, participated in this population-based cross-sectional study embedded within the Korean Genome Epidemiology Study (KoGES). Based on at baseline and the last visit, the study participants were classified into four types of sleep initiation time: persistent late sleep (PLS), persistent usual sleep (PUS), persistent early sleep (PES), and non-persistent sleep (NPS) types. Metabolic syndrome was defined as having three or more of the following five criteria: abdominal obesity, impaired glucose intolerance, high blood pressure, high triglyceride, and low high-density lipoprotein-cholesterol. Among the 2674 study participants, the prevalence of metabolic syndrome was 865 (32.35%). To estimate the association between sleep initiation time and the risk of having metabolic syndrome, we constructed multivariable logistic regression models. After adjusting for covariates including sleep duration, the participants of the PLS type were 1.87 times more likely to have metabolic syndrome (odds ratio = 1.87, 95% confidence interval 1.07–3.27) than those of the PES type. In conclusion, in this population-based cross-sectional study, we observed that the PLS type of sleep initiation time had a significantly increased risk of metabolic syndrome as compared to the PES type, even after adjusting for covariates.