• The second-order polynomial regression model can well predict the thrust force, maximum hole wall temperature and delamination damage factor of both composites (4.3% -8.5% relative error). With the proposed hybrid optimization method, Pareto solutions which meet the temperature/delamination constraints are identified and the overall optimized performance with trade-off between hole quality and production efficiency has been achieved. The complex interaction between the design varibles and the objectives in composite drilling was visulaized for the first time through self-organizing map. By revealing the Pareto front of CF/PEKK drilling and comparing with that of thermoset CF/epoxy, we revealed the impact of different matrix properties (mainly toughness and thermal-mechanical properties)