Responsible utilization of natural mineral resources is essential for mitigating their imminent depletion. In this study, natural molybdenite (MoS₂) containing sulfur vacancies (MoS_(2−x)) is modified for the synergistic enhancement of electromagnetic wave (EMW) absorption. Under the influence of thermal motion, negative (O) and positive (Cu) ions are embedded in MoS_(2−x) to realize synchronous tunable ion and phase hybridization, affording MoS_(2−x)/Cu₂S/MoO₂ heterogeneous composites. Ion and phase hybridization considerably reduces the bandgap, changing the semiconductor type of MoS₂ from p to n. They also promote the generation of sulfur vacancies and a complex heterojunction, increasing the uneven charge distribution between the polyphase interfaces as well as increasing the number of active sites, thereby improving the probability of polarization. These processes enhance the EMW absorption properties of the Cu/O–codoped MoS₂ matrix composites. Negative (positive) ion and phase hybridization probably enhances the EMW absorption properties by increasing the number of defects and interfacial polarizations for which the heterogeneous structure provides the necessary microenvironment. Thus, this study considerably expands the application of molybdenite in high–efficiency EMW absorption materials and offers new perspectives on mineral resource utilization.