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.