The work aims to solve the problems of low automation, low efficiency and data inaccuracy in the logistics and warehousing of Chinese medicinal materials by conducting necessary digital and intelligent management, in order to improve efficiency and data accuracy. Combined with the circulation environment of Chinese medicinal materials and based on Radio Frequency Identification (RFID), Global Positioning System (GPS), Internet of Things (IoT) technology and temperature and humidity detection technology, an intelligent management system for logistics and warehousing of Chinese medicinal materials was designed and developed and an improved collision bit-based Hamming's heavy-count grouped query tree algorithm (HCQT) was proposed. The algorithm eliminated idle time slots and reduced collision time slots, which made the information collection and transmission of RFID system for Chinese medicinal materials more efficient. The management function of Chinese medicinal materials in all aspects of logistics and warehousing as well as temperature and humidity, data intelligent real-time update was realized and the algorithm was applied to real-time environmental monitoring. The system realizes the automated management of the logistics and warehousing of Chinese medicinal materials, improves the work efficiency, and has a good application prospect in a large number of intelligent packaging logistics system.