In response to the emergent public health event of COVID-19, the efficiency of transport of medical waste from hospitals to disposal stations is a worthwhile issue to study. In this paper, based on the actual situation of COVID-19 and environmental impact assessment guidelines, an immune algorithm is used to establish a location model of urban medical waste storage sites. In view of the selection of temporary storage stations and realistic transportation demand, an efficiency-of-transport model of medical waste between hospitals and temporary storage stations is established by using an ant colony-tabu hybrid algorithm. In order to specify such status, Wuhan city in Hubei Province, China-considered the first city to suffer from COVID-19-was chosen as an example of verification; the two-level model and the immune algorithm-ant colony optimization-tabu search (IA-ACO-TS) algorithm were used for simulation and testing, which achieved good verification. To a certain extent, the model and the algorithm are proposed to solve the problem of medical waste disposal, based on transit temporary storage stations, which we are convinced will have far-reaching significance for China and other countries to dispatch medical waste in response to such public health emergencies.