A methodology of building simulation models as applied to the thermal processes of machine tools in Simulink is presented. Three ways to building simulation models in Simulink are considered: by using the analytical solution of the thermal conductivity equation, tool for solving differential equations and apparatus of transfer functions. These three ways are presented for solving two typical problems: building the thermal characteristics of the machine tool under zero and non-zero initial conditions. Studies have shown that Simulink allows to build models with simple logic, but the advantage of the built S-models is their visibility and structuring. When modeling the diagrammatic works of the machine’s operation, the method of building simulation models based on the use of analytical solutions of the thermal conductivity equation allows to build the most compact models. A feature of building invariant models in Simulink is the use of the Matlab m-file, in which the parameters used in the S-model are generated.