As an important basis for the study of detection and mitigation of train operation conflicts (TOC), the analysis on generation causes and mechanism of TOC in high speed railway has important practical significance on realizing intelligent high-speed railway dispatching command. With train operation late as the necessary conditions for TOC, the analysis sorts out the main reasons for affecting TOC from such four aspects as equipment facilities, human behavior, external environment, and organization management and obtains 17 factors in the end. The Fuzzy Decision Making Trial and Evaluation Laboratory-Interpretative Structural Modeling (DEMATEL-ISM) is adopted to construct the adjacency matrix between the factors and calculate the reachability matrix and finally get a hierarchical and directed graph of the causes of conflicts through the hierarchy of factors. The results show that equipment facilities, transport organizations and dispatchers’ professional quality are the main reasons for TOC; natural environment, equipment operating environment, unexpected passenger flow and the psychological quality, educational level, years of service, etc. of dispatchers are the indirect causes of TOC; and working environment, the management of equipment and dispatchers and its mechanism are the deep-seated reasons for the TOC.