BackgroundThis study aimed to compare the cardio-metabolic, anthropometric, and liver function indices among metabolic obesity phenotypes.MethodsIn this cross-sectional study, which was carried out in Hoveyzeh, Khuzestan Province, Iran, a total of 7,464 individuals (male: 2859, female: 4605), were recruited and classified into four groups, based on Body Mass Index (obese, BMI ≥ 30 kg/m2; non-obese, BMI = 18.5–29.9 kg/m2) and the National Cholesterol Education Program and Adult Treatment Panel (NCEP ATP) III criteria (Healthy group, ≤ 1 of the criteria; Unhealthy group, ≥ 2 of the criteria), as follows: Metabolically Healthy Non-Obese (MHNO, 28.14%), Metabolically Unhealthy Non-Obese (MUNO, 33.06%), Metabolically Healthy Obese (MHO, 6.54%), and Metabolically Unhealthy Obese (MUO, 32.26%). Anthropometric indices (Waist/Hip Ratio (WHR), Waist/Height Ratio (WHtR), Body Adiposity Index (BAI), Visceral Adiposity Index (VAI), and Weight adjusted Waist Index (WWI)), cardio-metabolic indices (Atherogenic Index of Plasma (AIP), Lipid Accumulation Product (LAP), Cardio-Metabolic Index (CMI), Lipoprotein Combine Index (LCI), Triglyceride-Glucose (TyG), TyG-BMI, TyG-WC, and Thrombolysis In Myocardial Infarction (TIMI) risk index), and hepatic indices (Hepatic Steatosis Index (HSI) and ALD/NAFLD index (ANI)) were calculated and compared between the groups.ResultsWHR,VAI, AIP, LAP, CMI, LCI, TyG, and TIMI risk index values were significantly higher in the MUNO phenotype compared to the MHO phenotype (WHR: 0.97 vs. 0.95; VAI: 3.16 vs. 1.33; AIP: 0.58 vs. 0.25; LAP: 78.87 vs. 55.79; CMI: 2.69 vs. 1.25; LCI: 27.91 vs. 12.11; TyG: 9.21 vs. 8.41; TIMI: 18.66 vs. 15.63; p < 0.001). The highest and lowest HSI and ANI values were detected in the MUO phenotype. After adjustment for age, sex, physical activity, and years of education, VAI showed the highest Odds Ratio for MUNO (OR: 5.65; 95% CI: 5.12, 6.24) and MUO (OR: 5.40; 95% CI: 5.89, 5.95) compared to the MHNO phenotypes (p < 0.001). The ANI indices was associated with a reduced risk of MUO (OR: 0.76; 95% CI: 0.75–0.78), MUNO (OR: 0.88; 95% CI: 0.87–0.90), and MHO (OR: 0.79; 95% CI: 0.77–0.81) phenotypes (p < 0.001).ConclusionMUNO phenotype was exposed to a higher risk of cardiovascular disease compared to the MHO phenotype. VAI was found to be the optimal index for cardiovascular risk assessment.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12902-023-01372-9.