Dry hobbing is a new gear machining process with high efficiency and environmental friendliness, replacing traditional wet hobbing process. However, to get high reliable precision, it is a critical work for the dry hobbing system to reduce and control the thermal impact. Even new hobbing machine tool structure with high thermal stability such as double stand columns was designed to substitute the traditional structure; some new structures, such as air extraction and filtration device, air-cooling component, and magnetic chip conveyor, would affect the thermal energy accumulation of dry hobbing machine tool. In this paper, a multi-variable thermal energy control model was developed to describe the thermal energy accumulation characteristic of dry hobbing machine tool. Variables which would affect thermal energy generation and sink of dry hobbing machine tool are analyzed. A multi-objective optimization algorithm is proposed for variable optimization, combined with the multi-variable thermal energy control model. An application method is presented to show the thermal energy control procedure of dry hobbing machine tool. As a result, the temperature variation of interior space air, workpiece column, and anterior end cover is fluctuated in an acceptable range with optimization. Furthermore, thermal deformation errors, which range from −7 to 3 μm, could meet production requirements. It illustrates that the multi-variable driving thermal energy control model of dry hobbing machine tool is available.