This paper develops a three dimensional (3-D) finite element modeling (FEM) to predict the workpiece thermal distortion in minimum quantity lubrication (MQL) deep-hole drilling. Drilling-induced heat fluxes on the drilled hole bottom surface (HBS) and hole wall surface (HWS) are first determined by the inverse heat transfer method. The proposed 3-D heat carrier model consisting of shell elements to carry the HWS heat flux and solid elements to carry the HBS heat flux conducts the heat to the workpiece to mimic drilling process. A coupled thermal-elastic analysis is used to calculate the workpiece thermal distortion at each time step based on the temperature distribution. The heat carrier model is validated by comparing the temperature profiles at selected points with those from an existing 2-D axisymmetric advection model. The capability for modeling distortion in the case of drilling multiple deep-holes is also demonstrated.