Catch crop (green manure) planting is considered an efficient strategy to improve soil fertility in agro-ecosystems. Methane (CH₄) emissions from paddies subjected to continuous green manure amendment though is a topic that remains unexplored. To clarify the impact of continuous green manure amendment on rice yield and CH₄ emissions, a long-term trial (established in 2003, Yixing, China) was designed with the field observations conducted between 2019 and 2020. Two green manure crops (milk vetch, ryegrass) were selected as the catch crop with fallow as the control, all trialed at two N application rates i) low N dosage deriving from the optimum effect between yield-N fertilizer (LN, 200 kg ha^-1), and ii) a higher N dose as the empirical farmer's dose (HN, 270 kg ha^-1). The results showed that continuous green manure amendment notably increased soil organic carbon (SOC) compared to that of the control, while HN significantly increased the dissolved organic nitrogen compared to LN. The rice yield among treatments remained similar, ranging from 8.6 t ha^-1 to 9.4 t ha^-1 (two years’ average). CH₄ emissions were notably related to green manure, and remained unaffected by N application rate. Ryegrass amendment after 18 years remarkably stimulated the CH₄ emissions compared to other treatments, while the difference between milk vetch-amended and fallow treatments was found insignificant. Ryegrass increased soil mcrA gene with the abundance becoming the highest under HN. Methanogens abundance and SOC content were the main factors affecting CH₄ emissions under ryegrass addition. Moreover, the CH₄ emission intensity was aligned with CH₄ emissions mainly due to the similar rice yield. Overall, continuous milk vetch planting is a recommended catch crop strategy that increases soil fertility and maintains rice yield without increasing CH₄ emissions.