Abstract: In recent years, the development of ecological farms has emerged as a key focus in China’s pursuit of sustainable agriculture development. Among various innovative models, the ‘swine-biogas-fruit-electricity’ system has gained attention as an integrated ecological agricultural recycling system, combining livestock breeding, biogas production, fruit cultivation, and renewable energy generation. This model has been actively promoted in several regions as part of China’s green transition strategy. This study evaluates the comprehensive benefits of the “swine-biogas-fruit-electricity” ecological farming model from the perspectives of carbon emission reduction, economic performance, and dietary nutrient supply, using a case study from Rugao City, Jiangsu Province. Key indicators such as greenhouse gas emissions, production costs, profits, and nutrient supply were quantified. A multi-objective optimization model for ecological farm production structure was constructed based on the non-dominated sorting genetic algorithm (NSGA-Ⅱ), aiming to propose sustainable development solutions for ecological farming model. The analysis focuses on the cost-profit ratio and overall profitability of the farm. The study examines the system’s contribution to nutritional supply for local populations, a crucial indicator of food security and rural welfare. Using a case study from Nantong, Jiangsu Province, this research explores the model’s comprehensive benefits and sustainable optimization strategies. Compared to conventional farming systems, ecological farms achieve significantly lower carbon footprints, higher cost-effectiveness, and more efficient circular resource flows. The study showed that greenhouse gas emissions per unit area in the cropping system of the ecological farm were reduced by approximately 91% compared to conventional farms, while emissions per unit in the livestock system decreased by 2%, attributable to the internal cycling of energy and nutrients through biogas power generation and manure recycling. Economic Performance: The ecological farm achieved higher profits for most crops through cost control measures, with fruit cultivation generating 29%−50% higher net profits compared to conventional farms. Meanwhile, the livestock system reduced production cost by 46% compared to conventional farms, primarily through self-breeding practices. Although the ecological farm's dietary nutrient supply per unit area was slightly lower than that of conventional farms, it maintained stable supply levels. Further multi-objective optimization simulations revealed significant trade-offs and synergies in production structure adjustments under different goal orientations (maximizing yield, profit, or minimizing carbon emissions). By adopting different optimization strategies, the farm system can achieve up to a 56% reduction in greenhouse gas emissions, a 93% increase in total profit, or a 110% improvement in population-level nutritional supply, depending on the selected optimization approach. This study not only provides a theoretical foundation for optimizing the “swine-biogas-fruit-electricity” model but also offers practical insights for policymakers and agricultural practitioners. By quantifying the system’s benefits and identifying optimal production scales, the research contributes to the broader adoption and sustainable development of ecological farming in China. The findings hold significant value for promoting low-carbon agriculture, rural economic growth, and food security, aligning with China’s national strategies for green transformation and rural revitalization.