This paper presents a method to investigate the characteristics of a ball bearing and the dynamics of a HDD spindle system due to temperature variation. Finite element model is developed for the rotating and stationary parts of a HDD spindle system separately to determine their thermal deformations by using ANSYS, a finite element program. Then, the relative position of the rotating part with respect to the stationary part is determined by solving the equilibrium equation of the contact force between upper and lower ball bearings. The validity of the proposed method is verified by comparing the theoretical natural frequencies of a HDD spindle system with the experimental ones before and after temperature variation. It shows that the elevated temperature results in the increase of contact angle and the decrease of bearing deformation, contact force and bearing stiffness, which result in the decrease of the natural frequencies of a HDD spindle system.