This study provides new insights into the uncertainty quantification and reliability analysis of a flexible rotor system undergoing rub-impact. A probabilistic nonlinear formulation is proposed by considering the parameter uncertainties of different random distribution characteristics. The harmonic balance and alternating frequency/time (HB-AFT) scheme are employed to analyze the nonlinear behaviors of the system. To avoid the computationally intensive nonlinear calculations, the efficient Kriging surrogate strategy is adopted for the propagation of uncertainties in rotor dynamics, which enables rapid estimation of the statistics of nonlinear responses. Then, the probability density function (PDF) is evaluated for reliability analysis to determine the conditions for the occurrence of the rub-impact fault. Numerical results are compared with experimental results and those obtained by Monte Carlo simulation (MCS) to verify the effectiveness of the new modeling. Effects of stochastic parameters on vibrational behaviors and reliability of the rub-impact rotor system are finally performed, which demonstrates the proposed method is high-efficiency and high-precision for predicting the high-nonlinearity between output response and input variables. This contribution will further enrich the theory and application of probabilistic statistical analysis and reliability evaluation for complex rotating machinery.