The present study examined the association between low-carbohydrate diet (LCD) score, glycemic index (GI), and glycemic load (GL) with visceral fat level (VFL) and lipid accumulation product (LAP). This cross-sectional study was conducted on 270 adults (118 men and 152 women) aged between 18–45 living in Tehran, Iran, between February 2017 and December 2018. Dietary intake was assessed using a validated semi-quantitative food frequency questionnaire (FFQ). Body composition were also assessed. We used analyses of covariance and binary logistic regression to explore associations after controlling for age, energy intake (model 1), education, smoking status, physical activity, occupation, marriage and metabolic diseases. There were no significant differences between tertiles of GI, GL and LCD for means of anthropometric measures, LAP and VFL index in men, while women in the highest tertile of GI and GL had significantly higher mean LAP in the crude model (P = 0·02) and model 1(P = 0·04), which disappeared after controlling for other confounders (P = 0·12). Moreover, the OR and CIs for having high LAP and VFL was not associated with dietary GI, GL and LCD in crude and adjusted models. However, chance of high VFL reduced by 65% and 57% among women with high adherence to LCD score (OR = 0·35, 95% CI = 0·16–0·78, P = 0·01) and model 1 (OR = 0·43, 95% CI = 0·18–1, P = 0·05), respectively. However, this significant association disappeared after controlling for other confounders (P = 0·07). Overall, we found carbohydrate quality and LCD score are not associated with LAP and VFL index. However, gender-specific relationship should not be neglect and warrants further investigation.