Because there were many random factors, the failure analysis and reliability analysis of stochastic structural system was very difficult. In this paper, failure procedure and reliability analysis flow chart of stochastic structural system based on stochastic finite element were present. Establishment of the safety margin, reduced member stiffness matrix and opposite sign of the equivalent nodal force was analyzed in the failure process. Stochastic finite element method was adopt to solve the structures’ stochastic, and the reliability of structural system is evaluated by PNET method. According to probabilities of the failure paths redound to probability of failure of the structural system, the most significant failure paths was determined on the basis of the branch-and-bound method. Then, a classical 48-bar space truss problem is made as an example to illustrate the predominance of this algorithm, the calculation shows that the analysis of the failure process is justified; this methodology is efficient and useful for reliability analysis of large stochastic structural system.