The functionalization of structural carbon fiber reinforced polymer (CFRP) composites remains a significant challenge. In this work, the integration of structure-function was achieved in carbon fiber reinforced PEEK (CF/PEEK) composite by introducing a ZnMn2O4-based interface with the functionalities of electromagnetic interference (EMI) shielding and thermal conductivity (TC). The ZnMn2O4 nanospheres/CF network was constructed by introducing ZnMn2O4 nanospheres on the CF surface, realizing a significantly strengthened composite interface. Notably, the interlayer shear strength (ILSS) of the UCF-Z125/PEEK composite has reached 85.38 MPa, marking a 47.51 % increase over the Unsized CF/PEEK composite. In addition, the EMI shielding and the TC performances of the CF/PEEK composite have also improved, with the EMI shielding of the composite enhanced by 54.67 % and the through-plane TC increased by 47.17 %. This structure-function integrated composite can be used not only as structural materials in aerospace applications but also as high-performance bifunctional materials in semiconductor and artificial intelligence industries.