In this study, a thermomechanical model is developed to simulate a finite drilling set of Carbon Fibre Reinforced Polymers (CFRP)/Titanium (Ti) hybrid structures widely known for their energy saving performance. The model applies different heat fluxes at the trim plane of the two phases of the composite, owing to cutting forces, in order to simulate the temperature evolution at the workpiece during the cutting step. A user-defined subroutine VDFLUX was implemented to address the temperature-coupled displacement approach. A user-material subroutine VUMAT was developed to describe Hashin damage-coupled elasticity model for the CFRP phase while Johnson–Cook damage criteria was considered for describing the behavior of titanium phase. The two subroutines coordinate to evaluate sensitively the heat effects at the CFRP/Ti interface and within the subsurface of the structure at each increment. The proposed model has been first calibrated based on tensile standard tests. The material removal process was then investigated versus cutting conditions. Predictions show discontinuity in temperature field at interface that should further favor damage to localize especially at CFRP phase. The obtained results highlight the significant effects of fibre orientation in dominating cutting temperature and thermal effects over the whole hybrid structure.