High-speed dry hobbing is an advanced green machining technology for gears. However, thermal issues in the machine tools become serious under the high cutting speed and dry cutting conditions, which result in a nonlinear evolution of the machine tool dynamics, and finally affect the hobbing stability. In view of this, introducing the hob spindle system as the object, this paper intends to investigate the influence of time-varying temperatures on the modal parameters based on the modal tests. Then, a temperature-dependent modal parameters prediction model based on the multi-output Gaussian process regression (MOGPR) is proposed. The experimental results indicated that the modal parameters of the spindle system vary obviously with changing thermal states. The natural frequencies for the first and third modes increased with the temperature rise, while the variation of the natural frequency for the second mode was insignificant. The damping ratios for the first three modes showed a decreasing trend with the temperature rise. The constructed MOGPR model has the capability to effectively predict the modal parameters with the time-varying thermal effects, which can provide a support to build the temperature-dependent hobbing stability boundaries.