The present study was aim to evaluate the association between very long chain saturated fatty acids (VLSFAs) and metabolic syndrome (MetS) in Korean population. The study population were recruited from the Korea National Health and Nutrition Examination Survey VI (2013). Using the cross-sectional study design, socio-demographic factors, medical history, and clinical measurements were investigated according to quartiles of VLSFAs intake. The associations between each and sum of VLSFAs intake and MetS were assessed by logistic regression. The result indicated that higher intake of VLSFAs was significantly associated with favorable metabolic status, including lower levels of circulating triglyceride (TG) (p < 0.05). Additionally, subjects with higher intake of arachidic acid and total VLSFAs were negatively associated with MetS risk compared to subjects with lower intake of those fatty acids (p < 0.05). In conclusion, dietary VLSFAs intake was associated with metabolic risk factors and lower risk of MetS in Korean population.