To understand the effects of waste amendments on microbiological mechanisms of methane emissions in paddy fields, the effects of single and mixed slag and biochar amendments on soil physicochemical properties were investigated in the elongation stage of both early and late paddy fields. Moreover, the diversity of methanogens and their community structures under different waste amendments were also investigated using PCR-RFLP and sequencing. The results showed that during the elongation stage of early paddy fields, both soil salinity and pH were significantly increased in mixed amendments. During the elongation stage of late paddy fields, soil salinity was significantly increased in mixed amendments, while soil pH was significantly increased in slag and mixed amendments. Shannon index (H') and Simpson diversity index (D) showed that the diversity of methanogens in soil treated with slag, biochar, and mixed amendments was higher than that of the control. Phylogenetic analysis showed that methanogeni communities in the paddy fields could be subdivided into six groups:Methanobacteriales, Methanomicrobiales, Methanosarcinales, Methanococcales, Methanocellales, and Methanomassiliicoccales. The most dominant methanogenic group was Methanomicrobiales. Comparison with the control, the relative abundance of Methanomassiliicoccus was lowered in the three types of treatments of the early paddy fields, and the relative abundance of Methanosarcina was lowered in biochar amendment. The relative abundance of Methanomassiliicoccus and Methanosarcina may have contributed to decreased CH₄ emissions.