The characteristics of urban rail transit emergencies include fast diffusion, wide-ranging influence and difficult handling. They require the coordination of multiple organizations. Previous studies have shown that the inter-organization collaboration efficiency is low. This article takes the subject of urban rail transit emergencies and studies the factors that influence inter-organization collaboration obstacles in emergency rescues, trying to reveal the formation path of interorganization emergency collaboration obstacles. The 25 factors that influence inter-organization collaboration obstacles, which are determined using interviews and a survey, are grouped into five major elements (emergency organization obstacles, emergency information obstacles, emergency resource obstacles, emergency plan obstacles and emergency command obstacles). A hypothesis model of the relationship among these factors is established based on emergency management theory and organization collaboration theory, and then empirical research is conducted using a structural equation model combined with large-scale questionnaires. Then the dynamic causal model of inter-organization collaboration obstacles is established through system dynamics to explore the formation mechanism of such obstacles. The results indicate that the five elements interact with each other, and that eliminating these obstacles, especially those in the emergency organization obstacles and emergency plan obstacles groups, is essential for improving the efficiency of emergency command and inter-organization collaboration.