The current knowledge regarding the effect of global climate change on rice-paddy methane (CH4) emissions is incomplete, partly because information is limited concerning the mechanism of the microbial response to elevated ground-level ozone (O3). A field experiment was conducted in the China Ozone Free-Air Concentration Enrichment facility in a rice-wheat rotation system to investigate the responses of methanogenic archaeal communities to elevated ground-level O3 by culture-independent and -reliant approaches. We found that elevated ground-level O3 inhibited methanogenic activity and influenced the composition of paddy methanogenic communities, reducing the abundance and diversity of paddy methanogens by adversely affecting dominant groups, such as aceticlastic Methanosaeta, especially at the rice tillering stage. Our results indicated that continuously elevated ground-level O3 would negatively influence paddy methanogenic archaeal communities and its critical ecological function. These findings will contribute to a comprehensive understanding of the responses and feedbacks of paddy ecosystems to global climate change.