This research investigates the vibration caused by ball bearing in a HDD spindle system, specifically non-repeatable runout (NRRO), at elevated temperature by analyzing the characteristics of ball bearing and the natural vibration characteristics of the spindle system due to the effect of elevated temperature. It shows that the elevated temperature results in the decrease of bearing deformation in the spindle system, which reduces the bearing stiffness and the natural frequencies of the spindle system consequently. It has a significant effect on the amplitude and the frequency distribution of NRRO at elevated temperature.