An interval analysis method of rotor transient response based on interval mathematics, Taylor expansions and perturbation theory is proposed to analyze the transient response of flexible rotors with uncertain parameters. As the specific probability distribution of uncertain parameters is not required, the interval analysis method is more suitable for practical use in comparison with traditional probability methods when dealing with the uncertain problems. Transient dynamic balancing method of flexible rotors based on transient response information was then introduced, and the simulation of a double-disc rotor with elastic supports was carried out. The influence of uncertainties on the balancing efficiency was analyzed by introducing uncertainties into the transient dynamic balancing process. The results show that the uncertainties can cause significant reduction in dynamic balancing efficiency and increasing of the residual vibration.