This is the first time multi-objective optimization is carried out for CFRTP drilling. A hybrid optimization algorithm integrating NSGA-II and TOPSIS is proposed for CF/PEKK drilling, with the aim of accurately predicting the drilling performance, obtaining the Pareto optimal solutions and ranking the multiple alternatives based on their proximity to ideal solutions. This work also presents the first comparative study on the optimal drilling conditions of carbon fibre composites containing thermoplastic and thermoset epoxy matrices respectively, (i.e., CF/PEKK vs. CF/epoxy), to verify the impact of different composite matrix thermalmechanical properties/machining performance on the final optimization outcome. By deploying the more the sustainable CF/PEKK composite and enhancing its manufacturing efficiency, we believe this work will have a long lasting impact on sustainable manufacturing of next generation composites and contribute to a greener aviation industry. This study will not only provide important parametric guidance for sustainable manufacturing of next generation CFRTP but will inspire new lines of research such as developing novel CFRTP cutting tools and predictive machining damage models for CFRTP. The main conclusions and future recommendations are as follows: