The article presents the approach and the thermal modeling technique of CNC machine tools, implemented at the stage of operation. In the work, as a practical implementation of the fast modeling technology, a simulation method based on the Matlab Simulink application was used. In the work to build a thermal model of the machine tool, we used analytical solutions of the heat conduction equation. This method is applied to the machine tool operating in conditions of variable thermal processes due to varying cutting speeds. The conditions for the coordination of the thermal characteristics of the machine tool at their boundaries, corresponding to the changing spindle rotation speeds, determine the peculiarity of their construction. A feature of the implementation of the mathematical model is the use of experimental modal analysis. In this case, the modal parameters of the approximating functions are determined by solving the optimization problem. To coordinate the adjacent thermal characteristics at their borders, a special condition was adopted. Regardless of the number of temperature modes used in the model, the initial level of the first temperature mode for the next mode of operation of the machine tool was taken to be equal to the achieved level of the thermal characteristic of the machine tool at the last time interval of the current mode of operation.