Transportation and logistics systems are becoming increasingly complex and critical to modern infrastructure. This paper proposes a novel AI-enhanced fault-tolerant control framework to address the dual challenges of physical malfunctions and cyber threats. By leveraging advanced machine learning algorithms and real-time data analytics, the proposed methodology aims to enhance the reliability, safety, and security of transportation and logistics systems. This research explores the foundations and practical implementations of AI-driven anomaly detection, predictive maintenance, and autonomous response systems. The findings demonstrate significant improvements in system resilience and robustness, making a substantial contribution to the field of intelligent transportation management.