In recent years, cities are threatened by various natural hazards. Planning emergency shelters in advance is an effective approach to reducing the damage caused by disasters and ensuring the safety of residents. Thus, providing the optimal layout of urban emergency shelters is an important stage of disaster management and an act of humanitarian logistics. In order to study the optimal layout of emergency shelters in small mountain cities, this paper constructs multi-level location models for different grades of emergency shelters so as to minimize the travel and construction costs and maximize the coverage rate. Specifically, the actual service of emergency shelters is determined using Geographic Information System (GIS) software and Weighted Voronoi Diagram (WVD) models under the limitation of site capacity, and the space layout is adjusted through combining the actual urban land with the construction position. In this paper, the Jianchuan county seat at Yunnan Province, China, was considered as a case study to illustrate the models of emergency shelters in which the feasibility of the presented models is verified. The proposed research methods and models have provided theoretical basis and a benchmark for the optimal layout of emergency shelters in other small mountain cities