Abstract: Ecological farms adopt environmentally friendly agricultural techniques such as green manure, straw returning 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 for promoting the application of composite ecological technology models. Therefore, this study focuses on ecological farms in Shanghai, using a combination of life cycle assessment and material flow analysis methods to compare the carbon footprints and nitrogen cycling efficiency of different types of ecological farms. Based on the scale of livestock farming, different proportions of organic fertilizer substitution (full substitution and 30% substitution) are set up to optimize farm carbon emissions. The results show that compared with plantation farms, integrated crop-livestock ecological farms simultaneously increase both carbon emissions and carbon sequestration, with higher carbon footprints per unit area. In integrated crop-livestock ecological farms, emissions from energy use and livestock farming processes account for more than 75% of total emissions. Among these, MCLS has 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 76.70 t(CO₂)·hm⁻² is the highest due to the scale of livestock farming and input of energy and materials. integrated crop-livestock ecological farms do not exhibit clear advantages in terms of carbon footprints per unit nutrient density and yield. Except for OR, other farms generally have excessive nitrogen fertilizer input, resulting in only about 30% nutrient utilization efficiency for the cultivation part of integrated farming and breeding farms and conventional farms, forming a high-input, low-output production model. However, integrated live-stock mode can improve nitrogen utilization efficiency to around 50% through waste resource recycling, indicating that integrated live-stock ecological farms can make more efficient use of resources invested. Under scenarios of fertilizer reduction and 30% organic fertilizer substitution for chemical fertilizers, the carbon emission intensity of all farms decreases by about 30%, suggesting that integrated farming and breeding ecological farms have great potential for emission reduction.