The Hani Terraces, classified as one of the globally important agricultural heritage systems (GIAHS), exhibit significant ecosystem service values. The adoption and encouragement of rice-fish co-cropping, an environmentally friendly agricultural practice, positively impact the enhancement of farmland water and soil resource utilization efficiency, as well as the value addition of agricultural products. Evaluating the carbon footprint and economic benefits of the rice-fish co-cropping can provide an objective assessment of its compatibility with the sustainable development of the Hani terraces, a traditional agricultural system. However, current research predominantly relied on field trials conducted in demonstration areas, which may not fully capture represent the actual production conditions of smallholder households. This study utilized micro-survey data collected from 385 farmers across 40 villages in 12 townships spanning 4 counties within the Hani terraces area as the research basis. Referring to the United Nations Intergovernmental Panel on Climate Change (IPCC) 2006 IPCC Guidelines for National Greenhouse Gas Inventories (2019 Revision), the carbon footprints of rice-fish co-cropping and rice mono-cropping modes were quantified and compared by employing the life-cycle assessment (LCA) methodology, while simultaneously calculating and net benefits and the net benefits considering carbon emissions for both modes. Results indicated that: (1) the rice-fish co-cropping mode in the Hani terraces exhibited excellent environmental benefits, with a lower carbon footprint per unit area of 5988.42kgCO2-eq/hm2, compared to 6347.90kgCO2-eq/hm2 for the rice mono-cropping mode. Additionally, the carbon footprints per unit of output value for rice-fish co-cropping and rice mono-cropping were 0.15kgCO2-eq/yuan and 0.22kgCO2-eq/yuan, respectively. (2) Further analysis showed that in the rice-fish co-cropping mode, the carbon footprint of the production process and agricultural inputs accounted for 60.19% and 39.81%, respectively, and CH4, N2O and fertilizer inputs were the important components of the carbon footprint, occupying 41.85%, 16.15% and 37.86%, respectively. For the rice mono-cropping mode, the carbon footprints of CH4, N2O and fertilizer inputs were 39.42%, 17.34% and 41.20%, respectively. (3) The net benefits of rice-fish co-cropping and rice mono-cropping were 26,911.46 yuan/hm2 and 19,049.66 yuan/hm2, respectively, and the net benefits considering carbon emissions were 26,531.02 yuan/hm2 and 18,646.37 yuan/hm2, respectively. Compared to rice mono-cropping, rice-fish co-cropping has higher economic benefits with less environmental impact. Based on this, this study suggests that the positive contribution of rice-fish co-cropping in agricultural carbon emission reduction should be emphasized and the key aspects of carbon emission reduction should be clarified, and the application of rice-fish co-cropping in the conservation and inheritance of the rice cropping system of the Hani terraces should be highlighted.