An objective and complete assessment of the carbon footprint of rice-fishery co-cropping model is critical for the rice-farming industry’s low-carbon and green growth. Based on field experiments and the life cycle assessment (LCA) methodology, a comprehensive carbon footprint assessment of rice monoculture, rice-shrimp co-cropping, and rice-crab co-cropping models was conducted in this study, and the NEEB of different rice farming models was calculated based on the economic benefits. The carbon footprints per unit area of rice monoculture, rice-shrimp co-cropping, and rice-crab co-cropping models were 14122.65 kg (CO₂-eq)·hm^-2, 13791.78 kg (CO₂-eq)·hm^-2, and 15617.13 kg (CO₂-eq)·hm^-2, respectively, according to the data. Hotspot analysis revealed that the carbon footprint composition of the rice-shrimp and rice-crab co-cropping models was influenced more by CH4 emissions, energy use, and feed inputs. Due to the greater economic production values of rice-shrimp and rice-crab co-cropping modes, the NEEB of these two modes increased by 81.45% and 69.52%, respectively, as compared to rice monoculture. Overall, rice-shrimp and rice-crab co-cropping models can reduce emissions and improve paddy field efficiency to some extent when compared to rice monoculture and rice-crab co-cropping models, but attention should be paid to the point of trade-off between carbon footprints and economic benefits in order to promote the green and efficient development of the rice-fishery co-cropping model. The technique utilized in this work can give technical assistance for a more thorough carbon footprint assessment of multifunctional agricultural production systems.