The effect of cutting temperatures on the hole quality in multi-layered carbon fibre reinforced polymer (CFRP)/Ti stacks was investigated. The cutting force, cutting heat, hole surface, and subsurface quality of CFRP during drilling with and without Ti alloy supporting layer were analyzed, and the evaluation method for subsurface damage was proposed. The results show the cutting temperature and subsurface quality are greatly influenced by the existence or absence of Ti alloy supporting layer, whereas the cutting force and surface quality are slightly affected. A large amount of cutting heat is generated during cutting process of CFRP and Ti alloy simultaneously, resulting in the significant increase in temperature at the exit part of CFRP holes. The high temperature reduces the rigidity and bonding performance of CFRP resin matrix, leading to serious subsurface damage of the fibre layers around the exit part of CFRP holes. The subsurface damage was also evaluated by the proposed method, and the fibre layer at the exit part of holes is the most damaged, and the farther the distance away from the exit part of holes, the less damaged the subsurface. Therefore, the cutting temperature significantly influences the subsurface quality of CFRP hole during the drilling of multi-layered CFRP/Ti stacks, and subsurface damage is crucial to evaluate the machining quality of CFRP.