This study investigates the effect of air pressure on workpiece temperature in through tool minimum quantity lubrication (MQL) deep-hole drilling. Experiments on 200 mm deep holes drilled by a 10 mm carbide drill were conducted under regular (500 kPa) and high (1000 kPa) air pressure conditions. Torque data shows that the chip clogging problem occurring under regular air pressure can be solved by the high air pressure. An inverse heat transfer method is utilized to quantify the heat fluxes and calculate the temperature distribution during drilling based on embedded thermocouples along the depth. Results show that temperature around the hole increases rapidly when the chips start accumulating in the hole under regular air pressure and cause high heat flux on the drilled hole wall surface. The high pressure condition, prevents chip accumulation, thus reducing the total heat flux.