An efficient post-processing simulation method is proposed to estimate small failure probabilities of stochastic dynamic structures involving the inherent randomness of structural physical-geometrical parameters and external excitations. To extract a small failure probability, the proposed method introduces an intermediate event to represent the realizations of extreme structural response in the tail of distribution. With the aid of this intermediate event, structural failure probability is reformulated as a product of the event’s occurrence probability and the conditional exceedance probability of extreme response when the event occurs. The latter corresponds to a distribution of extreme response under the condition of the intermediate event, referred to as the conditional extreme value distribution (CEVD). Accordingly, the proposed method is termed the CEVD method. To reconstruct the CEVD, a truncated shifted generalized lognormal distribution model is employed. Bayesian estimation method is utilized to determine the two shape parameters of this model based on the samples of both original extreme value distribution and CEVD, where the CEVD samples are generated by Markov chain Monte Carlo sampling. The efficiency and accuracy of the proposed method are demonstrated through two numerical examples considering seismic reliability analyses of a 10-story nonlinear frame and a soil-foundation-structure interaction system.