Green manure and rice straw recycling is widely practiced in paddy soils of southern China to enhance soil fertility and crop productivity; however, its environmental consequences remain lacking. Here, we used a long-term field experiment to quantify greenhouse gas (GHG) emissions and associated microbial functional genes, energy-use efficiency, carbon footprint, and net ecosystem economic benefit to assess the sustainability implications of this practice. The treatments consisted of conventional chemical fertilizers (CK), CK + green manure recycling (M), CK + early-season rice straw recycling (ERS), CK + ERS + late-season rice straw recycling (DRS), CK + ERS + M (ERSM) and CK + DRS + M (DRSM). Compared with ERS, DRS and DRSM, the ERSM significantly reduced the annual cumulative methane (CH₄) emissions by 24.3 %, 33.9 % and 22.1 %, respectively. Similarly, ERSM significantly reduced nitrous oxide (N₂O) emissions by 18.5 %–34.2 % compared to the other treatments, except for DRS. However, compared with all the other treatments, the ERSM treatment increased annual grain yield by 6.0 %–67.6 %, energy-use efficiency by 6.8 %–68 %, and net ecosystem economic benefit by 10.9 %–112.1 %. Optimizing carbon-to-nitrogen ratio lowers direct GHG emissions through balancing CH₄-related gene activity (mcrA and pmoA) and by promoting ammonia-oxidizing genes (amoA), which in turn reduced carbon footprint. Soil organic carbon storage and CH₄ via direct-GHG emissions and chemical nitrogen via indirect-GHG emissions were the major contributors to carbon footprint. In conclusion, ERSM is an effective strategy to promote sustainable rice production in rice-rice cropping systems and it has the potential to support carbon neutrality efforts.