Abstract Background: Cardiometabolic multimorbidity is an increasing public health burden. This study aimed to evaluate the association of waist-to-height ratio (WHtR), waist circumference (WC) and body mass index (BMI) with risk of cardiometabolic multimorbidity. Methods: We used data from the China Health and Retirement Longitudinal Study (CHARLS). 10521 participants aged 45 and over were recruited, including 8807 individuals with 0 cardiometabolic disease at baseline (stage Ⅰ) and 1714 individuals with 1 cardiometabolic disease at baseline (stage Ⅱ). Logistic regression was conducted to estimate the odds ratios (ORs) and confidence intervals (CIs). Net reclassification index (NRI) and integrated discrimination improvement (IDI) were used to evaluate the incremental predictive value beyond conventional factors. Results: In stage Ⅰ, increased risk of cardiometabolic multimorbidity was observed among participants with WHtR ≥ 0.5 (OR: 1.76, 95% CI: 1.05–2.97), WC ≥ 85 (men) + WC ≥ 75 (women) (OR: 1.77, 95% CI: 1.05–2.97) or BMI ≥ 24 (OR: 1.48, 95% CI: 0.98–2.24). Furthermore, both NRI and IDI of WHtR and WC were higher than those of BMI. In stage Ⅱ, the adjusted ORs (95% CIs) of WHtR ≥ 0.5, WC ≥ 85 (men) + WC ≥ 75 (women), and BMI ≥ 24 were 2.04 (1.24–3.35), 2.07 (1.28–3.34), and 1.47 (1.06–2.04), respectively. In addition, WC exhibited the highest NRI and IDI. Conclusions: WHtR, WC and BMI are independent predictors of cardiometabolic multimorbidity in middle-aged and elderly Chinese population. WHtR and WC show better abilities in predicting cardiometabolic multimorbidity than BMI.