Patients at risk of chronic kidney disease (CKD) must be identified early and precisely in order to prevent complications, save lives, and limit expenditures for patients and health systems. This study aimed to develop a simple, high-precision machine learning model to identify individuals at risk of developing CKD in the near future, using a novel metabolic index with or without creatinine. This retrospective cohort study used data from the MJ medical record database collected between 2001 and 2015 in Taiwan. We used Cox hazard regression to identify potential predictors, including the novel metabolic index, for use as variables in the models. To develop a machine learning-based CKD risk model with fewer variables, we performed several experimental analyses to combine interacting variables into subsets. Those subsets were used to train three models, random forest, logistic regression, and XGBoost, with or without adding creatinine. The study included 12,189 participants, 20% with and 80% without CKD. The most important conventional predictors of CKD are age and gender. The novel metabolic index, TyG-Index, TG/HDL-ratio and VAI, had stronger predictive power than the conventional risk factors. Without including creatinine data, the XGBoost provided the best predictive performance. After adding creatinine, the performance of all the models was excellent, outperforming both conventional indicators and existing clinical algorithms for CKD. Using novel metabolic index in machine learning-based CKD risk prediction can accurately identify individuals at risk of diagnosis with CKD in the next year, with or without including creatinine.