This paper presents the three dimensional (3-D) finite element analysis (FEA) to predict the workpiece thermal distortion in drilling multiple deep-holes under minimum quantity lubrication (MQL) condition. Heat sources on the drilling hole bottom surface (HBS) and hole wall surface (HWS) are first determined by the inverse heat transfer method. A 3-D heat carrier consisting of shell elements to carry the HWS heat flux and solid elements to carry the HBS heat flux has been developed to conduct the heat to the workpiece during the drilling simulation. A thermal–elastic coupled FEA was applied to calculate the workpiece thermal distortion based on the temperature distribution. The concept of the heat carrier was validated by comparing the temperature calculation with an existing 2-D advection model. The 3-D thermal distortion was validated experimentally on an aluminum workpiece with four deep-holes drilled sequentially. The measured distortion on the reference point was 61 μm, which matches within uncertainty the FEA predicted distortion of 51 μm.