This study investigates the workpiece temperature in minimum quantity lubrication (MQL) deep hole drilling. An inverse heat transfer method is developed to estimate the spatial and temporal change of heat flux on the drilled hole wall surfaces based on the workpiece temperature measured using embedded thermocouples and analyzed using the finite element method. The inverse method is validated experimentally in both dry and MQL deep-hole drilling conditions and the results show good agreement with the experimental temperature measurements. This study demonstrates that the heat generated on the hole wall surface is significant in deep hole drilling. In the example of deep hole drilling of ductile iron, the level of thermal power applied on the hole wall surface is about the same as that on the hole bottom surface when a 10 mm drill reached a depth of 120 mm.