Abstract: Ecological farms adopt environmentally friendly agricultural techniques such as green manure, straw return to the field, integrated farming and breeding, and organic fertilizer substitution. These technologies can reduce fertilizer application and decrease non-point source pollution, but there is limited research on their impact on carbon footprint and nutrient utilization. Measuring the ecological benefits of ecological farms is crucial to promote the application of composite ecological technology. Therefore, this study focused on ecological farms in Shanghai, and used a combination of life cycle assessment and material flow analysis methods to compare the carbon footprints and nitrogen cycling efficiencies of different types of ecological farms, including diversified crop-livestock integrated eco-farm (MCLS), crop-livestock integrated eco-farm (CLS), organic rice farm (OR) and conventional rice farm (CK). Different proportions of organic fertilizer substituting for chemical fertilizer (full substitution and 30% substitution) with reduced fertilization amount were established based on the scale of crop farming to optimize farm carbon emissions. The results showed that compared with plantation farms, integrated crop-livestock eco-farms simultaneously increased both carbon emissions and sequestration, with higher carbon footprints per unit area. The rank of total carbon emissions for four types of farm was CLS (3 508.24 t CO₂) > MCLS (1 736.47 t CO₂) > OR (232.60 t CO₂) > CK (104.21 t CO₂), that of carbon footprint per unit area was MCLS 76.69 t(CO₂)·hm⁻² > CLS 50.29 t(CO₂)·hm⁻² > OR 21.04 t(CO₂)·hm⁻² > CK 13.63 t(CO₂)·hm⁻². Among these, MCLS had the highest carbon sequestration per unit area 11.58 t(CO₂)·hm⁻² and the lowest carbon emissions per unit output 2.10 t(CO₂)·(10⁴¥)⁻¹, but its carbon emission intensity 76.69 t(CO₂)·hm⁻² was the highest due to the scale of livestock farming and input of energy and materials. Integrated crop-livestock ecological farms did not exhibit clear advantages in terms of carbon footprint per unit nutrient density unit and yield. Emissions from energy use and livestock farming processes accounted for more than 75% of the total emissions in the integrated crop-livestock ecological farms; while carbon emission from materials input of the plantation farms accounted for 40.61%−50.78% of the total emission. Except for OR, other farms generally had excessive nitrogen fertilizer inputs, resulting in lower than 30% nutrient utilization efficiency for the cultivation part. However, the integrated crop and livestock mode can improve nitrogen utilization efficiency to approximately 50% through waste resource recycling, indicating that integrated crop-livestock eco-farms can make more efficient use of the resources invested. The carbon footprint intensity of all farms decreased by approximately 30% under the scenarios of fertilizer reduction and a 30% substitution of organic fertilizer for chemical fertilizers. This suggested that ecological farms have great potential for emission reduction through adjusting fertilization practices and energy utilization methods.