Abstract: Comprehensive planting and breeding in rice field makes full use of resources, and rice and aquatic animals are mutually beneficial, which is a typical green rice cultivation method. Methane emission from paddy fields is the main source of agricultural methane emission, and rice-crayfish coculture is a model with the largest application area of ecological cultivation of paddy field. Straw returning is an important operation of rice-crayfish model. Rice-crayfish coculture affects the physical and chemical properties of paddy soil by changing field engineering and straw organic matter input, and then affects methane emission. In order to research the effect and mechanism of long-term straw returning on methane emission on rice-crayfish coculture in rice season, this experiment designed four treatments in 2015: rice-crayfish and straw returning (RC-S), rice-crayfish and straw removing (RC-NS), rice-monoculture and straw returning (RM-S), rice-monoculture and straw removing (RM-NS), monitoring methane emission after 7 years, measuring and analyzing soil carbon pool index and functional microorganisms (mcrA and pmoA). The results show that the cumulative methane emission is RM-S, RC-S, RM-NS and RC-NS in turn. Compared with the rice-monoculture, the methane emission of the rice-crayfish coculture was significantly reduced by 15.00%, however, the methane emission of straw returning increased significantly by 31.79%. The results of path analysis show that the direct effects of total organic carbon (TOC), microbial biomass carbon (MBC), dissolved organic carbon (DOC) and methanogenic bacteria (mcrA) on methane emission are positively promoted, while the direct effects of Easily oxidizable organic carbon (ROC) and methanotrophic bacteria (pmoA) are negatively inhibited. Our research results show that the methane emission reduction mechanism of rice-crayfish coculture lies in increasing ROC content in soil and decreasing the abundance of functional gene mcrA of methanogenic bacteria, However, straw returning can increase methane emission by reducing the ROC content and mcrA gene abundance and increasing the DOC content. Therefore, rice-crayfish coculture can alleviate the methane emission effect caused by straw returning to the field. This study provides data support for rice-crayfish coculture to reduce emissions and increase efficiency.