Graphene-based supercapacitors have emerged as a promising candidate for energy storage due to their superior capacitive properties. Heteroatom-doping is a method of improving the capacitive properties of graphene-based electrodes, but the optimal doping conditions and electrochemical properties are not yet fully understood due to the synergistic effects that occur. Many parameters, such as doping content, defects, specific surface area (SA), electrolyte, and more, could affect the capacitance (CAP). In this study, we use machine learning to solve these critical issues. We applied many models, such as Light Gradient Boost Machine, Extreme Gradient Boost, Polynomial Regression, Neural Network, Elastic Net, Lasso Regression, Ridge Regression, Random Forest, Support Vector Machine, K-Nearest Neighbors, Gradient Boost, AdaBoost, and Decision Tree, to find a suitable model for CAP prediction. Moreover, we enhance the prediction result by taking advantage of the top candidate model and creating a stacking concept (called "stacking models"). The SHAP value was used to identify the range of properties that affect CAP, and it was discussed in detail. Our results suggest that high-CAP graphene supercapacitors should have a large SA, with 4-5% nitrogen, 10-15% oxygen, high percentages of sulfur, a defect ratio close to 1, with acid electrolyte, and a low current density. These findings, along with the developed model and code, are expected to serve as a valuable computational tool for future electrochemical research from fundamental to applications.