To achieve high-quality heterojunctions between continuous carbon fiber reinforced polyetheretherketone (CCF30/PEEK) and titanium alloy, a laser direct joining method on the basis of the design and generation of embedded mechanical interlocks between metals and composites was proposed. Results suggest that the structure density of the pre-fabricated microcones on metal surface plays a significant role in determining the joining strength of the produced joints. High-strength heterogeneous joints were obtained due to the formation of strong mechanical interlocks between metals and composites. The maximum fracture strength of the joints reached over 52 MPa when the structure density of microcones was 8.2 cones/mm2. The fracture of the joints located at the interlayer of composites or the interfaces between metals and composites. This indicates that the joining strength of joints exceeds the interlayer bonding strength of CCF30/PEEK. The developed method shows great potential to construct high-quality heterogeneous joints between continuous fiber reinforced polymers and metals in the fields such as aerospace and automotive.