The synergistic combination of carbon nanotubes (CNTs) and ductile thermoplastic resin has shown large potential in the improvement of fracture resistance for the epoxy matrix composites using the interleaving toughening method in recent years. The hybrid structure of CNTs and thermoplastic resin in interlayers affects directly the interlaminar structure and the resultant crack propagation path of the interleaved composites. In this work, the CNTs and thermoplastic polyetherketone-cardo (PEK-C) were used to prepare the interlayer with different hybrid structures to interleave the carbon fiber reinforced epoxy composites and the influence of hybrid structure on the interlaminar structure and the fracture toughness was investigated. The results showed that PEK-C/CNT/PEK-C sandwich interlayer produced the best toughening effect in mode I interlaminar fracture toughness (G_IC) and the G_IC was 446.76 J/m ², increased by 138.11% compared to blank composites, which benefited from the multilayered structure in the interlaminar region formed during curing process and the resultant tortuous crack propagation.