The work aims to make use of IoT technology to improve equipment set and optimize the logistics system of disinfection equipment, in order to develop an intelligent logistics system of disinfection equipment with low pollution risk, high recovery and traceability rate. The independent influence factors of equipment pollution were determined by literature analysis. The equipment set was improved by radio frequency identification technology (RFID). The original logistics system was optimized through intelligent equipment. According to dynamic programming and Bayesian risk principle, the pollution risk function of disinfection equipment was constructed, then the lowest risk construction scheme under limited budget was calculated. The recovery rate and contamination rate of optimization before & after optimization were comparative analyzed. The optimization effect was verified. The calculation results showed that compared with the original system, the intelligent logistics system's equipment recovery rate was increased by 79.82%, the pollution traceability rate was increased by 81.18%, and the equipment pollution risk rate was reduced by 86.33%. Combined with the calculation results of instrument pollution risk function, it is concluded that under a certain budget condition, the model can calculate out an optimization scheme with the minimum pollution risk, and help managers to make decisions. It indicates that reasonable use of IoT technology to realize digital upgrade of disinfection equipment logistics system can not only improve data collection rate effectively but also improve the recovery rate and pollution traceability rate of equipment, and thus reduce the risk of equipment pollution.