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The train control system is a complex system, when on the failure analysis, the train control system itself characteristics determine the using traditional fault tree analysis of the fault can be induced in limitations. Introduced the Bayesian networks for this technology, make full use of its mature reasoning algorithm, learning ability is very strong, very complete theoretical basis of advantages, the fault tree of each section of the event tree using Bayesian network is described. Using Bayesian network toolbox(BNT) to train speeding the causation and fault diagnosis reasoning analysis, through the results of numerical calculation of the main causes of failure under different scenarios, and put forward the corresponding measures to reduce the probability of failure.