In order to solve the rapidly increasing domestic delivery volume and various problems in the recent metropolitan area, domestic researchers are conducting research on the development of “Urban Logistics System Using Underground Space” using existing urban railway facilities in the city. Safety analysis and scenario analysis should be performed for the safe system design of the new concept logistics system, but the scenario analysis techniques performed in previous studies so far do not have standards and are defined differently depending on the domain, subject, or purpose. In addition, it is necessary to improve the difficulty of clearly defining the control structure and the omission of UCA in the existing STPA safety analysis. In this study, an improved scenario table is proposed for the AGV horizontal transport device, which is a key equipment of an urban logistics system using underground space, and a process model is proposed by linking systematic STPA safety analysis and scenario analysis, and UCA and Control Structure Guidelines are provided to create a safety analysis.