In order to investigate the effect of co-existence of copper (Cu) and sulfur (S) in acidic paddy soils on greenhouse gas emissions, this study conducted an indoor flooding incubation experiment with thirteen treatments including CK, CuCl2, CuSO4 (5, 50, and 100mg Cu/kg), KCl, and K2SO4 (with anionic concentrations equal to that of the six Cu treatments), respectively. Urea was used as the nitrogen source. A total of 128d of incubation was prepared for sufficient aging of heavy metals in the soil. The results showed that acidic soils significantly promoted the release of available Cu (P2+ and SO42- addition, but the Cu-S coexistence treatment reduced the effectiveness of each other. Compared with CK, the treatments of 5mg/kg Cu and different concentrations of KCl and K2SO4 decreased CH4 and N2O emissions by 19.4%~56.2% and 36.1%~84.5%, but 50 and 100mg/kg Cu significantly increased CH4 and N2O emissions of 28.9% to 615.2% and 97.5% to 337.4% (P2SO4 treatments significantly reduced N2O emissions by 74.1% and 69.6% (P4emissions (P>0.05). Compared with CuCl2 treatment, medium and high concentration of CuSO4 treatments significantly reduced the emission of CH4and N2O (P4 emission by reducing the abundance of methanogenic archaea (mcrA) and methanogenic bacterial functional genes (16S rRNA-CH4). Moreover, the coexistence of Cu-S promoted N2O emission by increasing ammonia monooxygenase functional gene (AOB amoA) abundance during early incubation (0~35d), whereas increased nitrous oxide reductase functional gene (nosZ) abundance during late period (35~128d) to reduce N2O emission. This study shows that the variable valence anion can significantly affect the microbial process of greenhouse gas production involving heavy metal cations, and the study of this interaction process has profound significance for the correct evaluation of GHGs emissions from farmland soil polluted by heavy metal. © 2024 Chinese Society for Environmental Sciences. All rights reserved.