The work aims to solve the RFID tag conflict in the process of managing packaging box at current stage. Based on the analysis of the existing conflict resolution algorithm, a new anti-collision algorithm was designed and implemented with multi-thread technology, backward binary anti-collision algorithm and optimized data structure. The RFID reader sent a command of triples and responded the information at the conflict position. This process reduced the amount of transmission data; the command that RFID sent was stored by the stack to reduce the times of identifying conflicts; with the thought of multithreading, the labels were classified to shorten the processing time of conflicts. The simulation analysis showed that, the efficiency of the multi-threading backward binary RFID anti-collision algorithm could be increased by about 51%. The algorithm solves the problem of RFID tag conflict, improves the efficiency of reading and writing in the case of multiple labels, and well solves the problems regarding the function and performance of RFID tag in the packaging box management system.