This research investigates the non-repeatable runout (NRRO) of a HDD spindle system at elevated temperature by analyzing the characteristics of a ball bearing and the natural vibration characteristics of a HDD spindle system due to the effect of elevated temperature. It shows that the elevated temperature results in the increase of the contact angle and the decrease of the deformation of the ball bearing in a HDD spindle system. The variation of bearing frequencies, which are dependent on the cosine function of contact angle, is almost negligible at elevated temperature. However, the decrease of bearing deformation at elevated temperature reduces the stiffness of the ball bearing and the natural frequencies of a HDD spindle system consequently. The latter has a significant effect on the amplitude and the frequency distribution of NRRO at elevated temperature.