Microwave absorption (MA) materials possessing multifunctional capabilities are increasingly imperative to meet the demanding requirements of complex service environments, particularly those prone to biofouling. Conventional MA materials, however, have predominantly focused on achieving high absorption performance while largely overlooking the essential aspect of anti-biofouling properties. Herein, we rationally construct core–shell Cu/ZnO arrays (Cu/ZnO_ars) hybrid nanostructures on carbon foam (CF) to achieve enhanced MA performance and anti-biofouling property. The unique porous architecture of CF is conducive to its absorption of the energy carried by electromagnetic waves through multiple reflections and scattering. Additionally, Cu/ZnO_ars with abundant voids and high aspect ratios are uniformly distributed on the CF skeleton surface, forming numerous hetero-interfaces that significantly strengthen interfacial polarization. The resulting Cu/ZnO_ars/CF composite exhibits exceptional electromagnetic wave attenuation capacity, achieving a minimum reflection loss of −50.6 dB and a broad effective absorption bandwidth of 8.64 GHz at a low fill loading of only 3 wt.%. Furthermore, the composite demonstrates effective antibacterial and anti-algal capabilities. This study presents an effective strategy for designing carbon-based materials to simultaneously enhance MA performance and anti-biofouling property.