It is very complex problem that the reliability of aircraft wing box structural system with many random variables (such as area, thickness, material modulus, load etc.) is analyzed. In the paper, the reliability analysis method of aircraft wing box structural system is proposed based on the theory of structural reliability and stochastic finite element. The explicit expression of safe margin and the sensitivity of safe margin to each random variable are given, which improves the accuracy and efficiency of reliability calculation. The relationship of the level of failure path with structural system failure probability is discussion. The failure probability of element is calculated by using first order second moment method, and the main failure path of structural system is identified by using the advanced branch and bound method, and the failure probability of structural system is evaluated by using probabilistic network evaluation technique method. Numerical examples show that the method is of efficient and accurate, and the 3 or 4 level of failure path is acceptable for wing box structural system considering efficiency and accuracy.