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[Display omitted] • An improved Accimap framework is proposed for subway accident investigation. • A sub-system concept is introduced to model the multi-stage characteristics. • The internal logic of the Zhengzhou subway Line 5 waterlogging accident is analyzed. • The countermeasures taken by governments after the accident is summarized. The cause of major accidents provides valuable lessons for hazard prevention and management improvement. However, the investigation of major accidents in a social-technical system could be a challenge that requires inter-disciplinary approaches. Accimap, a system-oriented method in accident investigation, has been widely used around multiple industries. However, as a typical social-technical system with various internal and external interactions, system-oriented analysis has rarely been applied in subway systems. Therefore, the objective of this work is to enhance the Accimap framework to conduct a hierarchical investigation into the contributions of multiple factors to the Zhengzhou waterlogging accident and analyze the interconnections between factors during the accident's progression. To capture the multiple-stage characteristic of subway accidents, a sub-system concept is introduced. By studying the accident evolution in depot/construction subsystem, station/dispatch subsystem and tunnel/rescue subsystem, this work provides a detailed case study that reveals the underlying deficiencies in the emergency management of Chinese subway system. Besides, this work also reviewed the most important countermeasures and policies implemented by different levels of governments following the accident. By demonstrating the lessons learned from and improvements made after the major accident, the findings can support the accident prevention and policy making within the subway industry in the future. [ABSTRACT FROM AUTHOR]