In order to effectively reduce the probability of subway operation accidents and explore the key risk factors and multi-factor risk coupling mechanism during the subway operation period, this paper classifies the risk factors affecting subway operation safety into four categories of primary risk factors, personnel, equipment and facilities, environment and safety management, introduces the emergency management concept to identify 18 secondary risk factors, combines the improved fuzzy decision making test and evaluation laboratory (DEMATEL) and Explanatory Structure Model (ISM) to visualize the risk factor action relationship, construct a six-order hierarchical recursive structure model for subway operation accidents, explore the coupling relationship and effect between risk factors from the perspective of single factor, double factor and multiple factors, establish a coupling effect metric model based on Natural Killing Model (N-K), carry out coupling information interaction scenario combination and coupling effect quantification calculation, and finally integrate fuzzy DEMATEL-ISM-NK model to correct the centrality, determine the key risk factors in subway operation accidents from the perspective of macro and micro analysis, qualitative and quantitative research, and propose safety prevention and control strategies accordingly. The results show that six factors, such as emergency management and social environment, are key risk factors to be prevented in the metro operation system. Multi-factor risk coupling leads to a higher probability of subway operation accidents, and controlling multi-factor involvement in coupling is an effective means to reduce the occurrence of subway operation accidents.