Complex urban systems, such as multi-floor rail transit stations and integrated railway transport hubs, are termed “complex urban public spaces” (CUPSs). These CUPSs facilitate people’s lives, but, at the same time, are threatened by various risks due to their multi-floor structure, dense crowds, high correlation in multi-function, complex facilities, and space openness. The risk events of CUPSs could have a negative influence on public safety and further influence sustainable development. Increasing the resilience of CUPSs is an effective way to respond to risks and guarantee public safety. Therefore, it is necessary to first assess the resilience of CUPSs. In this paper, a six-level comprehensive resilience indicator system was established based on aspects of the essence of resilience. Used in combination with the methods of resilience impact score and fuzzy analytical hierarchy process, the resilience value could be calculated. The Shenzhen North Railway Station (SZ) and the Guangzhou South Railway Station (GZ) were used to validate the proposed methodology. The established resilience indicator system was shown to be comprehensive and innovative, and, regarding practicality, the proposed assessment methodology is convenient to use. This research can help policymakers to assess the resilience of CUPSs and develop relevant policies to improve the resilience of buildings, which can further enhance urban sustainability.