To detect and mitigate the operation conflicts of high-speed trains, it is critical to clarify the generation mechanism of train operation conflicts (TOCs) in high speed railway (HSR). Taking train delays as the precondition of the TOCs, this paper sorts out the main causes of the TOCs into four aspects, namely, equipment facilities, human behaviour, external environment, and organization management, and obtains a total of direct and indirect impact factors for HSR TOCs. Then, the interpretative structural modelling (ISM) was adopted to construct the adjacency matrix between these factors, and calculate the reachability matrix. On this basis, a directed hierarchical graph was plotted for the TOC causes based on the hierarchical relationship between the factors. The results show that HSR TOCs are directly caused by equipment facilities, transport organizations, and dispatcher professionality, and indirectly induced by natural environment, equipment operating environment, unexpected passenger flow, as well as the psychological quality, educational level, and years of service of dispatchers; in addition, the working environment, and the management of equipment and dispatchers are the deep-seated reasons for the TOCs. The research results provide new insights into the intelligent dispatching command of the HSR.