Abstract: Fish–lotus coculture (LFC) is widely recognized as an economically efficient integrated ecological farming model; however, its effects on greenhouse gas emissions from aquaculture ponds remain poorly understood. In this study, we investigated the impacts of fish–lotus coculture on sediment organic carbon fractions and methane (CH₄) emissions in aquaculture ponds, with conventional aquaculture ponds serving as the control. The results showed that during the summer high-temperature period, both bubbles and diffusive CH₄ fluxes in LFC ponds were significantly lower than those in the control ponds (P<0.05). Meanwhile, lotus planting substantially altered the sediment carbon pool composition: particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) significantly increased by 51.35% and 168.89%, respectively (P<0.05), accompanied by a significant elevation in the MAOC/SOC ratio. Additionally, the copy number of the pmoA gene in the sediment of the LFC group was significantly higher, while the mcrA gene copy number was significantly lower than those in the control (P<0.05). Correlation analysis revealed that CH₄ flux was significantly negatively correlated with sediment MAOC content, and pmoA abundance was highly significantly positively correlated with POC, MAOC, and MAOC/SOC (P<0.01). Our results indicate that lotus planting drives marked CH₄ mitigation via the dual pathways of carbon pool stabilization and microbial community modulation (promoting methanotrophs while inhibiting methanogens), offering a promising new avenue for achieving low carbon sustainability in pond aquaculture.