Our study employs cross-efficiency analysis (CEA) and machine learning techniques to optimize supply chain performance. By integrating inverse DEA models with directional distance functions, we measure operational efficiency across various decision-making units (DMUs), accounting for undesirable outputs such as excess costs and emissions. Our results indicate a 20% improvement in market recognition efficiency and a 15% increase in earnings persistence efficiency after model application. Additionally, machine learning classifiers, including Random Forest and Support Vector Machines, further enhanced predictive accuracy, with Random Forest achieving the lowest mean absolute error of 0.07. These findings underscore the effectiveness of advanced analytical models in improving supply chain resilience and decision-making accuracy, contributing to sustainable operational performance.