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During the COVID-19 pandemic, disposable masks, protective clothing, gloves, and nasopharyngeal swabs collected by nucleic acid testing formed a large amount of medical waste. Medical waste has strict temporary storage time requirements in hospitals, which need to be transported to medical waste disposal plants within the specified time. However, as most of disposal plants are far away from downtown, they also need to be responsible for the transportation and disposal of medical waste in many hospitals, and put forward higher requirement for transportation routes. Rapid and safe disposal of all types of medical waste generated by COVID-19 is crucial to the prevention and control of the epidemic. This paper designs the transportation route optimization model using Anylogic simulation software based on the regional distribution of 118 tertiary hospitals and 2 large medical waste disposal plants in Beijing, China. At the same time, transportation routes of 118 tertiary hospitals in the morning peak, evening peak, all-day, and ordinary periods were simulated based on the Beijing traffic index in 2017. On this basis, through the analysis of the simulation data, the selection of medical waste transport routes for 118 tertiary hospitals in the morning peak, evening peak, all day, and ordinary periods is further clarified, so as to ensure that medical waste can be transported to the medical waste disposal plant in the shortest time. The shortest path and fastest speed transport mode, medical waste transport data set, and the selection of transport mode of 118 tertiary hospitals formed by this research provide certain reference experience for the rapid and safe transport of medical waste during the epidemic period, and also provides corresponding data support for medical waste transportation management in the post-epidemic era and medical waste transportation decision-making when facing major public health problems. [ABSTRACT FROM AUTHOR]