• Flexible and waterproof NCNT arrays on carbon fiber (NCNT@CF) were fabricated. • NCNT@CF exhibited excellent EMW absorption performances. • The R L,min value and EAB 10 of NCNT@CF are − 57.8 dB and 4.5 GHz, respectively. • RCS values of the materials were simulated under real far field conditions. • NCNT@CF had flexible, waterproof, and electric-thermal conversion functions. It is highly desirable, but challenging to develop multi-functional electromagnetic wave (EMW) absorbing material for practical applications in some special environments. Herein, we successfully fabricated cobalt-nanoparticle-embedded N-doped carbon nanotube arrays on the carbonized cotton fiber cloth as multifunctional material with an excellent EMW absorption, flexibility, hydrophobicity, and electric-thermal performance. The excellent multifunction benefits from high conductivity, large specific surface area, abundant N dopants, and three-dimensional open porous features. Minimal reflection loss and efficient absorption bandwidth of the optimized material as EMW absorbers can reach − 57.8 dB and 4.5 GHz, respectively, which are better than most reported carbon-based absorbers. Meanwhile, theoretical simulations of the radar cross-sectional (RCS) further confirm that the multifunctional material has excellent EMW attenuation performance and potential in practical application. Moreover, the materials possess strong hydrophobicity and high electrical conductivity, endowing them with other attractive functions of self-cleaning and good electric thermal performance, which expand the potential applications range of EMW absorption materials. Our present method can be extended to design next-generation EMW absorbing materials with multifunctionalities for practical applications in harsh environments.