Iron phthalocyanine (FePc) with self-assemble properties was used to construct microstructures on carbon fiber (CF). Morphology, roughness and wettability of modified CF were characterized. Then, poly(arylene ether nitriles) (PEN) was chosen to fabricate CF reinforced composites and the interfacial compatibility of composites was investigated by SEM and their viscoelastic properties. Rheological properties including linear viscoelastic region, storage/loss modulus, and viscosity were investigated. Besides, dynamic mechanical properties of the composites were studied under different frequency and the apparent activation energy of glass transition was calculated. Results showed that using a proper PEN solution concentration to impregnate FePc microstructures modified CF could help to form better mechanical interlocking on interface. Besides, influence of shape, size and density microstructures on forming mechanical interlocking was studied and discussed. Results revealed that granule-like microstructures, reducing the size of microstructure, and decreasing the distance between microstructures were benefit to forming better mechanical interlocking on interface. Based on the researches, mechanism of improved interfacial compatibility through forming mechanical interlocking was proposed and the interlaminar shear strength (ILSS) of the composites were studied.