Abstract: Comprehensive planting and breeding in rice fields make full use of resources. A typical green rice cultivation method involving rice and aquatic animals is utilized since they are mutually beneficial. Methane emissions from paddy fields are the main source of agricultural methane emissions, and rice-crayfish co-culture is a model with the largest application area for the ecological cultivation of paddy fields. Straw return is important in rice crayfish models. Rice-crayfish co-cultures affect the physical and chemical properties of paddy soils by changing field engineering and straw organic matter input, thereby affecting methane emissions. To study the effect and mechanism of long-term straw returning on methane emission from rice-crayfish coculture in the rice season, four treatments were designed in 2015: rice-crayfish coculture and straw returning (RC-S), rice-crayfish coculture and straw removing (RC-NS), rice-monoculture and straw returning (RM-S), and rice-monoculture and straw removing (RM-NS). Methane emission, and the soil carbon pool index and functional microorganisms were monitored after 7 years. The results showed that, compared to the rice monoculture, the methane emissions of the rice-crayfish coculture were significantly reduced by 1.42%−26.44%; however, the methane emissions of straw return significantly increased by 15.18%−54.36%. Path analysis showed that the direct effects of total organic carbon (TOC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), and methanogenic bacteria (mcrA) on methane emissions were positively promoted, while the direct effects of easily-oxidizable organic carbon (ROC) and methanotrophic bacteria (pmoA) were negatively inhibited. Our research results show that the methane emission reduction mechanism of rice-crayfish coculture lies in increasing the ROC content in the soil and decreasing the abundance of the functional gene mcrA of methanogenic bacteria; however, straw return can increase methane emissions 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.