Industrial structure systems may have non-linearity, and are also sometimes exposed to the danger of earthquake. In the design of such system, these factors should be accounted for from the viewpoint of reliability. This paper proposes a method to analyze seismic response and reliability design of a complex non-linear structure system under random excitation. The actual random excitation is represented to the corresponding Gaussian process for the statistical analysis. Then, the non-linear system is subjected to this random process. The non-linear structure system is modelled by substructure synthesis method (SSM) procedure. The non-linear equations are expanded sequentially. Then, the perturbed equations are solved in probabilistic method. Several statistical properties of a random process that are of interest in random vibration applications are reviewed in accordance with the non-linear stochastic problem. The system performance condition in the design of system is that responses caused by random excitation be limited within safe bounds. Thus, the reliability of the system is considered according to the crossing theory. Comparing with the results of the numerical simulation proved the efficiency of the proposed method.