In emergency medical facilities location, the hierarchical diagnosis and treatment system plays an obvious role in the rational allocation of medical resources and improving the use efficiency of medical resources. However, few studies have investigated the operational mechanism of hierarchical medical systems in uncertain environments. To address this research gap, this paper proposes a hybrid approach for emergency medical facilities’ location-allocation. In the first stage, in order to concentrate on the utilization of medical resources, we choose alternative facility points from the whole facilities through the entropy weight method (EWM). In the second stage, uncertainty sets are used to describe the uncertain number of patients at emergency medical points more accurately. We propose a robust model to configure large base hospitals based on the robust optimization method. Furthermore, the proposed robust models are applied to the emergency management of Huanggang City under COVID-19. The results show that the optimal emergency medical facility location-allocation scheme meets the actual treatment needs. Simultaneously, the disturbance ratio and uncertainty level have a significant impact on the configuration scheme.