To address the tractor-container binding problem in drop-and-pull transportation scenarios, this paper proposes an automatic tractor-container binding identification method based on multi-source perception fusion and implements a corresponding application system. The system integrates RFID, Bluetooth, and container positioning devices to determine whether a tractor and a container are bound, enabling automatic identification and dynamic management of binding relationships throughout the entire transportation process. In terms of identification strategy, a hierarchical decision-making and fusion verification mechanism is adopted. Through cross-validation of multi-source data, the reliability of identification results is significantly improved. When the reader fails to return data or is offline, the system can perform identification based on the trajectories of tractors and containers, thereby ensuring continuity and stability of the identification process. This approach effectively reduces the impact of complex environmental factors and wireless network fluctuations on identification results, improves binding identification accuracy, and enhances logistics transportation efficiency. A one-month large-scale test was conducted in real-world drop-and-pull transportation scenarios. The system achieved a binding record accuracy rate of 98.04%, according to the test, demonstrating the system’s feasibility and usefulness in actual engineering applications. The system offers dependable technical assistance for sophisticated, data-driven drop-and-pull transportation management.