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Quinones, redox-active functional groups in soil organic matter, can act as electron shuttles for microbial anaerobic transformation. Here, we used 13CH4 to trace 13C conversion (13C-CO2 + 13C-SOC) to investigate the influence of an artificial electron shuttle (anthraquinone-2,6-disulfonate, AQDS) on denitrifying anaerobic methane oxidation (DAMO) in paddy soil. The results showed that AQDS could act as the terminal electron acceptor for the anaerobic oxidation of methane (AOM) in the paddy field. Moreover, AQDS significantly enhanced nitrate-dependent AOM rates and the amount of 13C-CH4 assimilation to soil organic carbon (SOC), whereas it was remarkably reduced nitrite-dependent AOM rates and 13C assimilation. Ultimately, AQDS notably increased the total DAMO rates and 13C assimilation to SOC. However, the electron shuttle did not change the percentage of 13C-SOC in total 13C-CH4 conversion. These results suggest that electron shuttles in the natural organic matter might be able to offset methane emission by facilitating AOM coupled with the denitrification process.