With the increasing demand for effective electromagnetic wave (EMW) absorbers due to the proliferation of electronic devices and 5G communication systems, traditional wave-absorbing materials can no longer meet the current requirements. Thus, this research introduces a three-dimensional (3D) composite material consisting of PMMA@Mxene@Co₃O₄ microspheres, prepared through in situ self-assembly and hydrothermal growth. The strong electrical conductivity of Mxene, combined with the magnetic loss of Co₃O₄, ensures enhanced dielectric–magnetic synergy, leading to excellent EMW absorption. The study investigates the influence of varying Co₃O₄ content on the electromagnetic properties of the composite. Experimental results show that the optimal sample, with a thickness of 2.5 mm, achieves a minimum reflection loss (RLmin) of −52.88 dB at 6.88 GHz and an effective absorption bandwidth (EAB) of 5.28 GHz. This work highlights the potential of 3D PMMA@Mxene@Co₃O₄ composites as high-performance microwave absorbers, providing a promising solution to EMW pollution. The findings offer valuable insights into material design strategies, demonstrate a promising pathway for developing lightweight, high-performance EMW absorbing materials by optimizing impedance matching and utilizing advanced microstructure design techniques.