Aim: Cardiometabolic multimorbidity (CMM) is increasingly prevalent in China’s aging population, posing major public health challenges. Developing machine learning (ML) models for early prediction is essential to inform prevention. Methods: We used data from 16,970 adults aged ≥ 45 years from the China Health and Retirement Longitudinal Study (CHARLS) across four waves (2011-2018). We used 42 predictors from 2013/2015 (demographics, lifestyle factors, physical measures, and blood biomarkers) to train five ML models: generalized linear model (GLM), gradient boosting machine (GBM), distributed random forest (DRF), deep learning (DL), and a Stacked Ensemble model. The primary outcome was CMM in 2018, defined as self-reported diagnoses of ≥ 2 conditions among hypertension, diabetes, heart disease, and stroke. Models were evaluated using the area under the curve (AUC), Brier score, and calibration curves. Synthetic Minority Over-sampling Technique (SMOTE) and 5-fold cross-validation were used to optimize performance. Results: The Stacked Ensemble model achieved the best internally validated predictive performance (AUC = 0.755), significantly outperforming GLM and DL (both DeLong’s P = 0.03), with comparable performance to GBM and DRF. Calibration analysis confirmed reliable prediction (Brier score = 0.153). Variable importance analysis based on GBM and DRF identified dyslipidemia, age, triglycerides, high-density lipoprotein cholesterol, waist circumference, self-rated health expectations, pain, cooking fuel type, weight change, and cystatin C as the top-ranked predictors common to both algorithms. Conclusion: ML algorithms, particularly ensemble models, can effectively predict CMM risk in China’s aging population. The integration of diverse health indicators and self-perceived health measures enhances predictive power.