In order to obtain the thermal characteristics of the spindle–bearing integrated system of the computer numerical control (CNC) machine tools effectively, a mathematical model is established by employing the heat source method (HSM). The thermal characteristics of spindle–bearing system are identified by using the derived mathematical formula, and the presented model is validated by the finite element method (FEM) under four types of conditions corresponding to different heat intensities, heat transfer coefficients, geometrical model sizes, and heat source positions. Compared with the FEM, the presented model has better computational efficiency. The temperature fields of the two spindle systems of a CNC machine tool are predicted by using the present model. The predicted temperature field is compared with the measured data and results show that the maximum relative errors for the two systems are 0.41% and 8.38%, respectively. The proposed model has a potential to be applied in calculating temperature field and thermal deformation or other related engineering area.