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 MoS 2 /Cu 9 S 5 with multilevel honeycomb structures (X-MoS 2 /Cu 9 S 5 MHs, X = P, Si, Ge) were designed by space-confined growth and in situ sulfidation of a polyoxometalate-based metal−organic framework. X-MoS 2 /Cu 9 S 5 MHs possess low density, high surface area, and abundant cationcuprum and anion-sulfur double vacancies (V Cu and V S ) simultaneously that are unmatched by conventional EMWA materials. Also, the systematic investigation of the doping effect of various polyoxometalate heteroatoms on V Cu and V S 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.