Abstract: The emissions of greenhouse gases from agricultural ecosystems account for 12% of the total amount of global anthropogenic greenhouse gas emissions. However, as one prominent agricultural ecosystem, the fate and mechanisms of greenhouse gases (CH₄, N₂O, and CO₂) linked with the microorganisms and agricultural emission reduction strategies are still unclear at the soil-water interface in paddy fields.This work discussed the mechanisms and influencing factors of greenhouse gas (CH₄, N₂O, and CO₂) production in paddy fields, as well as agricultural management measures to reduce emissions. Researches demonstrated that the greenhouse gas emissions at the water-soil interface in paddy fields were primarily driven by microorganisms. The soil physicochemical properties, such as soil temperature, moisture, and redox potential (Eh), profoundly influenced the composition and processes of microbial communities, thereby affecting greenhouse gas emissions. Agricultural management measures, such as effective water regulation, soil nutrient management, and microbial regulation, can alter the flux of greenhouse gas emissions from the soil. Microbial regulation techniques, such as the addition of Bacillus amyloliquefaciens, stimulation of methane-oxidizing bacteria activity, and the exploration of nitrogen-fixing bacteria containing N₂O reductase genes, have promising potential for greenhouse gas emissions reduction. However, the microbial mechanisms of greenhouse gas emissions in paddy fields is currently primarily reliant on indoor studies and lacks the support of large-scale field data. The relationship between the microbial communities in rice fields and ecosystem functions, as well as the microbial control mechanisms mediated by agricultural management, are topics that have received little attention in the literature. Soil microorganisms play an important regulatory role in reducing greenhouse gas emissions in rice field soil. They can reduce greenhouse gas emissions by changing soil properties and altering the composition of microbial communities at the water-soil interface. This provides new perspectives for reducing greenhouse gas emissions in rice fields and provides theoretical support for reducing greenhouse gas emissions from farmland and mitigating global warming.