Trinitarian designs in the morphology, components, and microstructure remain challenging for advanced electromagnetic wave absorption (EMWA) materials with light weight, strong absorption, and well-defined structure-function relationships. Herein, a series of X-doped MoS2/Cu9S5 with multilevel honeycomb structures (X-MoS2/Cu9S5 MHs, X = P, Si, Ge) were designed by space-confined growth and in situ sulfidation of a polyoxometalate-based metal-organic framework. X-MoS2/Cu9S5 MHs possess low density, high surface area, and abundant cation-cuprum and anion-sulfur double vacancies (VCu and VS) simultaneously that are unmatched by conventional EMWA materials. Also, the systematic investigation of the doping effect of various polyoxometalate heteroatoms on VCu and VS in the microhoneycomb has been conducted. Experimental results and density functional theory calculations reveal that the excellent EMWA performance (-56.21 dB) results from the synergistic effect of morphology design, component optimization, and vacancy regulation. This study not only provides an important opportunity to understand a morphology-component-microstructure strategy in electromagnetic wave absorption but also builds a noteworthy bridge between bioinspired engineering and microscale absorbers.