In order to improve the operation efficiency of CR Express and play its important role under the "One Belt And One Road" initiative, the FTA-BN model is used to analyze and evaluate the clearance time risk of CR Express. First, the structure of Bayesian network was formed by fault tree model mapping and the probability of initial conditions is obtained. The EM algorithm is used for parameters learning based on actual data. Then the complete Bayesian network evaluation model was formed by updating parameters of nodes. Finally, the clearance time risk of CR express was analyzed in various aspects, and relevant risk events including customs declaration and order review are determined as the key influencing links for clearance efficiency. The paper also provides a reliable means for risk assessment of CR Express.