Polymeric metal-organic framework (MOF)-derived composites are promising functional materials because of their exceptional chemical homogeneity, designable components, and adjustable pore size. The modulation of oxygen and Mn vacancies via the introduction of heteroatoms and changes in the annealing temperature in MOFs-derived composites can be a possible solution to investigate the polarization loss mechanism, which facilitates the improvement of electromagnetic loss capacity. Herein, the design of laminate-stacked sphere-shaped trimetallic CoNiMn-MOFs is presented. The derived CoNi/ MnO@C composites retain the original topography of the MOFs. The concentration of oxygen vacancies increases with the incorporation of heteroatoms, but decreases with annealing temperature, which prevails in the polarization loss mechanism rather than the contribution of Mn 2+ vacancies and heterogeneous interfaces. Therefore, the minimum reflection loss of the CoNi/MnO@C sample demonstrates −55.2 dB at 2.6 mm and the broad effective absorption bandwidth reaches 8.0 GHz at 2.1 mm. This work is expected to provide meaningful insights into the significant effect of ion vacancy modulation on the EM wave-absorbing performance of Mn-based MOFs-derived composites.