【Objective】This study was designed to investigate the long-term effects of straw returning on methane (CH4) emissions in rice paddies and their microbial driving mechanisms to provide a theoretical basis for optimizing long-term straw returning management and synergistically achieving “carbon sequestration and emission reduction”.【Method】Based on a continuous 13-year (2006-2018) field experiment with rice-wheat rotation, four straw returning gradients were established: S0 (control at 0?t·hm-2), S1 (1.6?t·hm-2), S2 (3.2?t·hm-2), and S3 (4.8?t·hm-2). The changes in CH4 emissions during the rice season (2017-2018) and related soil environmental factors were observed.【Result】The results showed a significant positive correlation between straw returning amount and cumulative CH4 emissions, with the cumulative emissions in S1, S2, and S3 treatments increasing by 166%-219%, 420%-527%, and 660%-785% compared to S0, respectively. The microbial mechanism lies in the fact that straw input enhances soil organic carbon and dissolved organic carbon content while reducing soil redox potential, creating a strongly anaerobic environment. This significantly increases the abundance of methanogenic functional genes (mcrA) (with average increases of 2.5, 3.8, and 3.6 times compared to S0 for S1, S2, and S3, respectively) and enriches the Methanosarcinaceae family, which metabolizes multiple substrates, leading to a substantial increase in CH4 production potential (S3 increased by 246% compared to S0). Although the abundance and oxidation potential of methanotrophic functional genes (pmoA) also increased, the growth was far lower than the production potential, resulting in a metabolic imbalance of “more production than oxidation”, further exacerbating net CH4 emissions. Although S3 could enhance soil carbon sequestration rates, it had the highest mitigation benefit offset rate (12.93). In contrast, under conditions where there was no significant difference in mitigation benefit offset rates, S1 achieved the lowest CH4 emission coefficient (5.05%), while S2 achieved the highest carbon sequestration rate (2.27?t?CO2-eq t·hm-2·a-1), indicating that moderate straw returning optimally synergizes carbon sequestration and emission reduction. 【Conclusion】The results of this study reveal that moderate straw returning is a key measure to reconcile the contradiction between “carbon sequestration” and “emission reduction” in rice paddies.