Abstract: Rice-crayfish coculture has recently been developed owing to its high economic benefits. In 2020, the area used for rice-crayfish coculture in China reached 1.26×10⁶ hm². The objective and comprehensive evaluation of the carbon footprint of rice-crayfish coculture is crucial for low-carbon green development of the integrated farming industry of rice and aquaculture animals. Sensitivity and uncertainty analyses of carbon footprint can help to increase the robustness of the evaluation results and provide a reference to further optimize parameters and reduce the uncertainty of evaluation results in the future. Based on a field experiment and life cycle assessment (LCA), a comprehensive carbon footprint evaluation of rice monoculture and rice-crayfish coculture was carried out using 1 hm² (area), 1 ¥ (output value), and 1 NDU (nutrient density unit) as the functional units (FU). The results showed that the carbon footprint per hectare (CF_A) of rice monoculture and rice-crayfish coculture was 14 126 kg(CO₂-eq)·hm^–2 and 13 140 kg(CO₂-eq)·hm^–2, respectively; the latter was 7.0% lower than the former. Compared with rice monoculture, rice-crayfish coculture had higher economic output value and nutrition density delivery. Thus, the carbon footprint per output value 0.11 kg(CO₂-eq)·¥^–1 and carbon footprint per NDU 3.05 kg(CO₂-eq)·NDU^–1 of rice-crayfish coculture was 49.3%–81.4% lower than those of rice monoculture, whereas the net ecosystem economic budget (NEEB) of rice-crayfish coculture (85 745 ¥·hm^–2) was 511.5% higher than that of rice monoculture. Hotspot analysis showed that CH₄ emissions, electricity consumption, and feed input contributed greatly to carbon footprint, accounting for 59.8%, 13.8%, and 12.3%, respectively. The application of urea, compound fertilizer, and organic fertilizer contributed 4.7%, 3.8%, and 1.5% to carbon footprint, respectively; and N₂O emissions, diesel consumption, and rice seeds contributed even less (3.3%, 0.3%, and 0.4%, respectively). Sensitivity analysis showed that the carbon footprint was most sensitive to CH₄ emissions. When CH₄ emissions varied by ±40%, the carbon footprint varied between 9994 and 16 283 kg(CO₂-eq)·hm^–2. Carbon footprint was also sensitive to electricity consumption and feed input. When these two parameters were varied by ±40%, the carbon footprint varied from 12 413 to 13 864 kg(CO₂-eq)·hm^–2 and 12 491 to 13 787 kg(CO₂-eq)·hm^–2, respectively. Other parameters (i.e., diesel consumption, organic fertilizer, and rice seed inputs) had a weaker impact on the carbon footprint. The results of uncertainty analysis showed that the mean value of the carbon footprint of rice-crayfish coculture was 13 302±1166 kg(CO₂-eq)∙hm^–2, and the median and coefficient of variation were 13 250 kg(CO₂-eq)·hm^–2 and 8.76%, respectively, indicating a weak variation. Under 95% confidence interval, the CF_A of rice-crayfish coculture varied between 11 179 and 15 613 kg(CO₂-eq)·hm^–2. The results of this study highlighted the rich nutritional output function of rice-crayfish coculture and analyzed the urgency and necessity of transforming traditional agriculture to ecological agriculture from the perspective of improving the dietary structure of residents. The methods used in this study can provide technical support for a more comprehensive carbon footprint evaluation of agricultural production systems with multi-functional outputs.