Background High concentrations of mercury intake from seafood are known to cause various side effects in humans, including on the nervous system. Various studies have reported the effects of mercury concentrations in humans; however, the association between dyslipidemia, a cardiovascular disease risk factor, and mercury remains controversial. Therefore, this study aimed to investigate the association between mercury accumulation and cholesterol concentrations in a Korean population. Methods We analyzed data of a sample of 3,228 respondents obtained from the Korean National Environmental Health Survey cycle 3, surveyed between 2015 and 2017, to determine how lipid profiles changed according to the blood mercury concentrations (BHg) and urine mercury concentrations (UHg). Multiple regression analysis was used to determine the effects of mercury concentrations among various factors affecting blood cholesterol levels. Results The arithmetic mean (AM) of BHg was 2.91 (2.81–3.02) μg/L, and the geometric mean (GM) was 2.71 (2.59–2.85) μg/L. The AM of UHg was 0.52 (0.48–0.56) μg/L, and the GM was 0.35 (0.33–0.38) μg/L. Lipid profiles were more related to the BHg than to the UHg. Total cholesterol (total-C), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels increased significantly as BHg increased in males, and total-C, triglyceride, and LDL-C levels increased significantly in females. Multiple regression analysis indicated that BHg were significantly associated with total-C, HDL-C, and LDL-C levels. Conclusions We found an association between mercury exposure and the risk of dyslipidemia; however, further studies are required to elucidate a causal association.