This paper analyzes and summarizes the innovation and advancement of the collection-transportation system and disposal of medical waste in Honghe（Red river）hazardous waste and clinical waste disposal center，and introduces the exploration and practice of the classified collection-transportation，reverse logistics and cooperative disposal of the medical waste in this disposal center. After implementing the classification and classification collection of medical waste，establishing a scientific and reasonable reverse logistics system for the collection，transportation and disposal of medical waste，and adopting the mode of cooperative disposal of medical waste，the transportation cost of the medical waste was reduced the effectively，and the timely and safe disposal of clinical waste was guaranteed. It provides a reference for China’s medical waste collection and disposal industry.