To ensure public safety and protect property, the presence of urban commercial building shelters is very important. Decisions regarding the spatial layout of and division of responsibility for indoor emergency shelters involve several factors, i.e., population density, building environment, evacuation methods, and so on. To date in China, the design of these shelters and research in their regard has been limited, and the safety of personnel in commercial building is at stake. In this paper, we propose a spatial design for indoor earthquake emergency shelters located in commercial buildings. To realize evacuation efficiency, we designed an optimal zoning model for a shelter based on the P-median model. After model calculation and analysis, we obtained the optimal position of the isolation layer in a commercial building, and designed the interior space of an emergency shelter. Lastly, we determined the practicality of the design by analyzing the accessibility of the shelter. The results of the simulation experiment prove that the emergency shelter designed in this study is accessible to a wide urban area, can serve a large number of people, and demonstrates good performance.