Hybrid structures consisting of carbon fiber reinforced plastics (CFRP) and metal have been widely applied in aircraft manufacturing. Numerous holes need to be made in order to assemble the structures. Due to the small size of CFRP chips and the dry cutting conditions, improperly dealing with chips can increase tool wear, degrade hole quality, and contaminate to environment and health. In this study, an assisted chip removal system, mainly including an exhaust hood, a vacuum cleaner, and a tool holder, was used for helical milling of CFRP and titanium alloys (CFRP/Ti stacks). The geometry of the chip exhaust hood model was designed and optimized to clear and collect cutting chips using finite element method (FEM). Based on this system, pressurized air was pumped into cutting areas through the inner cooling channels in the tool. Then, the performance of the assisted chip removal system was evaluated in helical milling of CFRP/Ti stacks under different chip collecting conditions. Results showed that this system had a good ability of chip removal and preventing chips returning into the hole. And the pressurized air could promote chips remained in the hole to be removed and provide cooling effect to cutting tool. As a result, tool wear was reduced, the cutting force and cutting temperature were decreased, and hole quality was improved. Results proved the assisted chip removal system can help to further improve the hole-making process of CFRP/Ti stacks.