Due to the exist of the inevitable dimensional tolerance and assembling errors in the ball bearing, the interference amounts between the inner ring and the connected shaft are uncertain but bounded, which could directly affect the dynamics performance of the rotor-ball bearing system. Whereas, most of the works on the field of dynamics in a ball bearing have considered the varying compliance (VC) vibration as deterministic vibration and there are few quantitative studies considering the uncertain factors. Therefore, in this paper, an uncertain ball bearing-rotor dynamic model is presented based on the Chebyshev interval method. Firstly, the uncertain interference amounts between the bearing inner ring and the connected shaft are modeled by the Chebyshev interval method. Then the radial clearance and actual interference amounts of ball bearing are derived by the bearing-shaft interference fit model. The time-dependent ball-raceway contact probability is formulated and the influence of the average and deviation coefficient of the initial interference amounts on the vibration behaviors of the rotor under various rotational speeds are investigated based on the double degrees of freedom (2-DOF) ball bearing system. The numerical cases show that the amounts of the bearing-shaft interference fit are uncertain and could be affected by rotational speed, which have an obvious influence on the dynamic performance of the rotor-ball bearing system. Reasonable design of the interference amounts could reduce the dispersion of the displacement and time-varying stiffness. The numerical results obtained by the present study are compared to the Monte Carlo simulation (MCS), which show the validity of the study.