The thermal characteristics of the spindle system for CNC machine tools are influenced by multiple factors which are nonlinear and time-varying. In this paper, a nonlinear time-varying thermal characteristics solving model for the spindle system was established based on the numerical solution method. Through theoretical deduction and data fitting, mathematical models of nonlinear time-varying factors including the friction torque generated by lubricants, convective heat transfer coefficient, and coolant and ambient temperature are constructed. The temperature and displacement of the spindle system at each time step are solved by considering the comprehensive effect of multiple nonlinear time-varying factors. And the actual temperature and axial deformation data of the spindle system are obtained through thermal characteristics detection experiments. By comparing solution results affected by multiple nonlinear time-varying factors and by non time-varying factors with experimental data, it can be concluded that the nonlinear time-varying thermal characteristics model has advantages in reflecting the trend of numerical changes and the accuracy of result solving over a method considering non time-varying factors and the solution values of temperature affected by multiple nonlinear time-varying factors are almost consistent with detection values and the relative errors are all within ±3%. The relative error of axial deformation between the value solved by the model and the detection value is close to −1%. This conclusion demonstrates the rationality and accuracy of the thermal characteristics solving model and the construction of nonlinear time-varying factors. This study is of great significance for exploring the thermal characteristics of the spindle system and improving CNC machine tool performance in depth.