<p>The effective design of tool geometry and optimization of process parameters play a pivotal role in mitigating damage such as tearing, burrs, and delamination during the drilling of braided carbon fiber reinforced polyether ether ketone (BCF/PEEK). This study introduces a novel method for selecting optimal drilling tools and damage prediction analysis in BCF/PEEK drilling. First, a scale-span drilling finite element (FE) model is established based on an analysis of twist bit geometry and BCF/PEEK composition. Simulation and experimental validation identify the causes of damage in prefabricated holes. Subsequently, three innovative types of drilling tools are evaluated based on factors such as hole morphology, thrust force, and delamination. Finally, regression models are established to correlate damage factors, thrust force, and process parameters. The research findings indicate that using twist drill bits results in higher thrust forces, which lead to delamination defects at hole exits. Conversely, employing a tapered drill-reamer could enhance the exit quality of prefabricated holes, consistently maintaining damage factors below 1.14 under identical process parameters. The proposed method effectively predicts optimal process parameters, with a maximum error of only 0.276% in drilling BCF/PEEK.</p>