Epidemiological studies on the association between the low carbohydrate diet (LCD) score and CVD risk factors have limited and inconsistent results. Data are from the baseline survey of Community-based Cohort Study on Nervous System Diseases. A total of 4609 adults aged ≥ 18 years were included in the study. Dietary data were assessed using a validated semi-quantitative FFQ. Multivariable logistic regression analyses were used to estimate relationships of three LCD scores with low HDL-cholesterol, high LDL-cholesterol, hypercholesterolaemia, hypertriacylglycerolaemia, impaired fasting glucose (IFG), high blood pressure and hyperuricaemia after adjusting for potential confounders. A higher LCD score was negatively associated with low HDL-cholesterol (OR: 0·65 (95 % CI 0·50, 0·83), P = 0·0001) and IFG (OR: 0·65 (95 % CI 0·51, 0·81), P = 0·001) after the final adjustment. However, there are sex differences in this result. Males in the highest quintile of the animal-based or plant-based LCD scores showed a decreased risk of low HDL-cholesterol, and females in the highest quintile of the animal-based or plant-based LCD scores showed a decreased risk of IFG than those in the lowest quintile of the LCD scores. These results suggest that sex differences should be considered when using LCD to treat dyslipidaemia and reduce fasting blood glucose.