In the rural side, there is the absence of centers for cardiovascular ailment. Due to this, around 12 million people passing worldwide reported by WHO. The principal purpose of coronary illness is a propensity for smoking. ML classifiers are applied to predict the risk of cardiovascular disease. However, the ML model has some inherent problems like it’s serene to feature selection, splitting attribute, and imbalanced datasets prediction. Most of the mass datasets have multi-class labels, but their combinations are in different proportions. In this paper, we experiment with our system with Cleveland’s heart samples from the UCI repository. Our cluster-based DT learning (CDTL) mainly includes five key stages. At first, the original set has partitioned through target label distribution. From the high distribution samples, the other possible class combination has made. For each class-set combination, the significant features have identified through entropy. With the significant critical features, an entropy-based partition has made. At last, on these entropy clusters, RF performance is made through significant and all features in the prediction of heart disease. From our CDTL approach, the RF classifier achieves 89.30% improved prediction accuracy from 76.70% accuracy (without CDTL). Hence, the error rate of RF with CDTL has significantly reduced from 23.30 to 9.70%. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.