These days, most machine tools are interlocked by an enclosure for safety control. At that time, internal heat generation in machine tools first causes thermal deformation of the machine structure, which reduces the machining accuracy of the workpiece. Furthermore, the internal heat generation heats the air inside the enclosure, causing a heat build-up phenomenon, and the trapped heat causes re-thermal deformation of the machine tool structure. As a result, machine tools with enclosures are subject to extremely complex thermal deformation. On the other hand, we would like to use FEM thermal simulation to study thermal deformation countermeasures for machine tools with enclosures at the design stage, but it is difficult to analyze the heat build-up phenomenon using conventional FEM thermal simulation. In this research, the new FEM thermal simulation technology for the heat build-up phenomenon was developed and heat build-up phenomenon in a CNC lathe with enclosure was calculated using the proposed FEM simulation technology. As a result, it had been concluded that the proposed FEM simulation could calculate with high accuracy for the phenomenon of heat build-up in a CNC lathe with enclosure, and the proposed technology is very effective in the design.