The global COVID-19 pandemic is having a significant impact on the development of many aspects all over the world. As an important part of public services, rail transit requires effective response countermeasures to control the spread of COVID-19. Considering the current development of the epidemic situation, this article discusses the characteristics of COVID-19 transmission and identifies vulnerable areas to target in order to prevent and control the spread of the epidemic in the rail transit system. Countermeasures adopted to prevent the spread of COVID-19 are analyzed in terms of external and internal categories, which were classified into six groups: passenger service, case care, information, staff, equipment and operation management. An evaluation architecture was also constructed, which was established from the perspective of effectiveness, economic efficiency, acceptability, privacy and so on. The effect of implementing the measures was evaluated by a social survey, and their advantages and shortcomings were analyzed, which can be used to guide future epidemic prevention and control for rail transit systems around the world. It is important to formulate a reasonable work schedule according to local conditions, providing a reference for rapid response to future public health emergencies of international concern.