The advanced electromagnetic applications urgently require high performance absorbers with sophisticated structural and compositional design. An effective strategy is to construct a three-dimensional hollow structure, with enhanced electromagnetic wave dissipation capacity over a wide effective absorption bandwidth. However, a major challenge remains due to a single loss mechanism system derived from the conventional hollow nanobox structure, which seriously causes impedance mismatch and lack of polarization centers. Herein, we innovatively construct novel hollow structure FeCo@C (CMFC) with crystalline/amorphous heterojunction FeCo/C particles by cation exchange method, thereby achieving enhanced electromagnetic wave absorption. The CMFC achieves Ku-band effective absorption with a reflection loss of −50.57 dB and effective absorption bandwidth of 5.35 GHz at 1.8 mm. The CMFC exhibits excellent microwave absorption performance due to the presence of crystalline/amorphous FeCo/C heterojunction, which is attributed to the balanced dielectric loss and optimized impedance matching characteristics. CST simulations demonstrate that the CMFC has a radar scattering interface reduction value as high as 26.12 dBm (Wu et al., 2023) [2] at a scattering angle of 0°. This work provides new ideas for the rational design of hollow nanostructures with heterojunction particles for efficient microwave absorption.