The co-cure joining of thermoset composites by thermoplastics is an advanced approach to develop robust composite joints. Herein, Polyethylenimine (PEI) and Polyetheretherketone (PEEK) polymers in a form of film, woven mesh, hollow mesh and carbon fibre reinforced plastic were utilised as interlayers for the co-cure joining of an aerospace composite. A cracked-lap shear test was used to investigate the fracture toughness and mechanisms of the co-cured composite joints under a mixed mode-I/II loading condition. The experimental results revealed that the insert of PEI and PEEK interlayers significantly enhanced the mix-mode crack resistance of the composite joints by different levels. The most remarkable increase in the crack initiation energy and crack propagation energy was 161% and 613%, respectively, that were obtained by adding the PEEK film interlayers. The main toughening mechanisms of the PEI film joined composites were crack-pining and matrix toughening of the PEI particles, which were formed by the diffusion of the PEI resins into the composite epoxy matrix during the curing process. Plastic deformation and fracture of the PEEK resins were the main toughening mechanisms of the composites that were co-cure joined by the PEEK films, woven meshes, hollow meshes and carbon fibre reinforced tapes. The crack resistance of the composite joints correlated well with the level of the PEEK fracture phenomena during the mix-mode fracture process.