It is a significant challenge to develop a fast carbon fiber (CF) surface modification method, especially for the high strength electromagnetic wave (EMW) absorption materials. Herein, magnetic CoOx nanoparticles are successfully synthesized and uniformly assembled on CF surface with high oxygen-containing groups by rapid ambient microwave carbon thermal shock (MCTS). The presence of oxygen defect sites on CF surface promotes CoOx nanoparticles nucleation. The number of oxygen defects and the types of magnetic nanoparticles on the CF surface effectively adjust the surface chemical activity and the electromagnetic properties of CF, which is conducive to improving the EMW absorption performance and interface compatibility of the CoOx nanoparticles modified CF reinforced polyamide 6 (CO@CF/PA6) composites. Compared with CO@CF-0 s/PA6, the tensile strength and modulus of CO@CF-3.5 s/PA6 composite are increased by 18.1 % and 18.6 %, respectively. It also displays a minimum reflection loss value (−59.9 dB) at a thinner thickness of 1.9 mm while the maximum effective absorption bandwidth reaches 5.02 GHz with a thickness of 1.8 mm. Its radar cross-section values exhibit less than −10 dBm2 at all tested detection angles. This rapid MCTS shows great potential for large-scale production of CF modification with low-cost, efficient and environmentally friendly process