Mechanistically, this study reconstructs the dominant methanogens under ammonia stress through insights from microbiomics, metagenomics, and metaproteomics. The research identifies Methanobacterium as a "pseudo dominant genus" under ammonia stress—large in population but low in contribution. The significant downregulation of electron transfer efficiency and methyl-reducing protein expression in Methanobacterium may be key factors limiting its activity. Conversely, the study confirms Methanothrix as the "true dominant genus" under ammonia inhibition—reduced in population but undiminished in contribution. Methanothrix expresses all proteins required for acetoclastic and hydrogenotrophic methanogenesis and upregulates functional proteins related to post-translational modifications, tRNA activation, and initiation complex formation during enzyme synthesis. Finally, metaproteomics unveiled the presence of "exceptionally active genera" with remarkably low community abundance—specifically, Methanolinea, Methanospirillum, and unclassified_f__Methanoregulaceae. Their protein expression levels in the methanogenesis pathway surpassed those of Methanobacterium, establishing them as the primary drivers of hydrogenotrophic methanogenesis.