The dynamic model of the flexible multibody systems (FMS) is usually the differential equations with time-variant, high nonlinear and strong coupling characteristics. The traditional reliability models are inefficient to solve these problems. And the reliability model is poor in accuracy and computational efficiency. Based on this point, a new stochastic surrogate model for time-variant reliability analysis of FMS is proposed. Combined model order reduction with generalized polynomial chaos, the stochastic surrogate model is established and the statistical characteristics of system responses are obtained. The calculation method of kinematic time-variant reliability is given. Finally, the effectiveness of the method is verified by a rotating flexible beam. The results show that this method has high computational accuracy compared with Monte Carlo method