Hydroxyapatite/polyether-ether-ketone (HA/PEEK) composites are promising prosthesis materials due to their biological activity, but they often have mechanical properties that fall short of clinical requirements, typically with HA content below 40 wt%. This study utilized a customized screw extrusion-based 3D printhead, incorporating carbon fiber (CF) to produce HA/CF/PEEK composites with enhanced mechanical properties and HA content up to 60 wt%. The investigation focused on the effects of HA and CF content on the crystallization process and mechanical properties. Results showed that HA and CF affect crystallization differently due to varying densities; a phase volume ratio above 20 % inhibits crystallization. The elongation at break for composites with 10 wt% HA was 27.9 %, a record for 3D-printed HA/PEEK composites. The tensile strength for composites with 10 wt% HA and 40 wt% CF reached 115.7 MPa, the highest among the tested three-phase composites. Data fitting indicated that the effects of HA and CF on strength are independent. The toughness decreases exponentially with increased reinforcing phase content. This study explored a new method for preparing HA/PEEK and HA/CF/PEEK composites, expanding the performance boundaries of PEEK composites, enhancing their potential applications in bone implants.