To date, the best obesity-related indicators (ORIs) for predicting hypertension, dyslipidaemia, Type 2 diabetes mellitus (T2DM) and multimorbidity are still controversial. This study assessed the ability of 17 ORIs [body mass index (BMI), body fat percentage (BF%), c-index, Clínica Universidad de Navarra-Body Adiposity Estimator (CUN-BAE), a body shape index (ABSI), body adiposity index (BAI), waist circumference (WC), waist-hip ratio (WHR), waist-to-height ratio (WHtR), body roundness index (BRI), abdominal volume index (AVI), triglyceride glucose index (TYG), lipid accumulation product (LAP), visceral adiposity index (VAI), Chinese visceral adiposity index (CVAI), waist triglyceride index (WTI) and cardiometabolic index (CMI)] to predict hypertension, dyslipidemia, T2DM, and multimorbidity in populations aged 40–69 years. From November 2017 to December 2022, 10,432 compliant residents participated in this study. Receiver operating characteristic curves were used to assess the ability of ORIs to predict target diseases across the whole population and genders. The DeLong test was used to analyse the heterogeneity of area under curves (AUCs). Multivariable logistic regression was used to analyse the association of ORIs with hypertension, dyslipidaemia, T2DM, and multimorbidity. The prevalence of hypertension, dyslipidaemia, T2DM, and multimorbidity was 67.46%, 39.36%, 12.54% and 63.58%, respectively. After excluding ORIs associated with the target disease components, in the whole population, CVAI (AUC = 0.656), BMI (AUC = 0.655, not significantly different from WC and AVI), CVAI (AUC = 0.645, not significantly different from LAP, CMI, WHR, and WTI), and TYG (AUC = 0.740) were the best predictor of hypertension, dyslipidemia, T2DM, and multimorbidity, respectively (all P < 0.05). In the male population, BF% (AUC = 0.677), BMI (AUC = 0.698), CMI (AUC = 0.648, not significantly different from LAP and CVAI), and TYG (AUC = 0.741) were the best predictors (all P < 0.05). In the female population, CVAI (AUC = 0.677), CUN-BAE (AUC = 0.623, not significantly different from BF%, WC, WHR, WHtR, BRI and BMI), CVAI (AUC = 0.657, not significantly different from WHR), TYG (AUC = 0.740) were the best predictors (all P < 0.05). After adjusting for all covariates, all ORIs were significantly associated with hypertension, dyslipidaemia, T2DM, and multimorbidity (all P < 0.05), except for ABSI and hypertension and BAI and T2DM, which were insignificant. Ultimately, after considering the heterogeneity of prediction of ORIs among different populations, for hypertension, BF% was the best indicator for men and CVAI for the rest of the population. The best predictors of dyslipidaemia, T2DM, and multimorbidity were BMI, CVAI and TYG, respectively. Screening for common chronic diseases in combination with these factors may help to improve the effectiveness.