Scrutinizing the electromagnetic wave absorption mechanism of sulfides remains a challenge due to the variability of the modulation of the crystal structure of the sulfides. To take advantage of this variability, nanosheet-assembled Cu9S5/CN composites with sulfur vacancies were prepared in this study by self-assembly synthesis and subsequent high-temperature heat treatment. Systematic studies show the phase transition-dependent induced decrease in the conductivity, the defect site-induced difference in the charge density, the weakened vacancy formation of defect polarization loss, and the influence of valence state on electric dipole polarization loss and interfacial polarization loss, making the optimization of the dielectric constant a significant positive effect on the improvement of impedance matching. This work provides a reliable example and theoretical guidance for the crystal structure design for the preparation of a new generation of efficient sulfide-based wave-absorbing materials.