Because of its large area and complicated space utilization, in the event of a disaster, rescue efforts in specific areas of Taipei Main Station would be difficult. In addition, rescue efforts are also difficult to implement, because each area is managed by different units. In order to ensure emergency and safe evacuation of passengers and reduce the loss of related property during a disaster, a suitable disaster prevention system is required. This study conducted risk assessment based on the triggering factors of disaster types over the years. After synthesizing the results of the disaster risk assessment, a disaster preparedness contingency plan was designed. According to the Incident Command System (ICS), this study formulated the usual management measures and emergency response procedures for various levels of disasters. When an accident occurs, the system can automatically initiate various emergency disaster relief measures, monitor the development of the incident, transmit disaster information, and coordinate disaster emergency response procedures. This study established a building information modeling (BIM)-based cyber-physical system (CPS) and intelligent disaster prevention system integrated under the overall management of the Intelligent Joint Emergency Operation Center. The “Taipei Main Station Intelligent Disaster Prevention System” can manage the disaster prevention and relief information of various business entities in a unified way, and provide an intelligent disaster prevention function integrating BIM and virtual reality (VR). This system is functionally verified through exercises such as short-circuiting of wires in advertising boxes, firefighter disaster relief drills, indiscriminate violent attacks, and demolition of explosives. In this study, ICS was established through expert interviews, disaster-causing factors over the years, and a cloud-based electronic management system was established in combination with the BIM platform. The system provides emergency and safe evacuation of passengers in the event of a disaster, and reduces the loss of related properties.