Abstract: In recent years, ecological farm development has emerged as a key focus in China’s pursuit of sustainable agricultural practice. Among various innovative modes, the “swine-biogas-fruit-electricity” system has gained attention as an integrated ecological recycling system, combining livestock breeding, biogas production, fruit cultivation, and renewable energy generation. This mode 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 mode 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 the ecological farm’s production structure is constructed using the non-dominated sorting genetic algorithm to propose sustainable development solutions for ecological farming modes. The analysis focuses on the cost-to-profit ratio and overall profitability of the farm. This study also examines the system’s contribution to the nutrient supply level of local populations, a crucial indicator of food security and rural welfare. Using a case study from Rugao City, Jiangsu Province, this study further explores the comprehensive benefits and sustainable optimization strategies of the mode. Compared with conventional farm, ecological farm achieved a significantly lower carbon footprint, 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 88% compared with conventional farm, whereas emissions per unit swine in the livestock system decreased by 2%, attributable to the internal cycling of energy and nutrients through biogas power generation and manure recycling. In terms of economic performance, the ecological farm achieved higher profits for the crops through cost-control measures, with fruit cultivation generating 29%–50% higher profits compared to conventional farm. Meanwhile, the livestock system reduced production cost by 46% compared with conventional farm, primarily through self-breeding practices. Although the ecological farm’s dietary nutrient supply per unit area was slightly lower than that of conventional farm, it maintained a stable supply. Furthermore, multi-objective optimization simulations revealed significant trade-offs and synergies in production structure adjustments under different goal orientations (maximizing yield, maximizing profit, or minimizing carbon emissions). By adopting different optimization strategies, the farm system could achieve up to a 55% reduction in greenhouse gas emissions, a 93% increase in total profit, or a 110% improvement in the level of dietary nutrient supply, depending on the selected approach. This study not only provides a theoretical foundation for optimizing the “swine-biogas-fruit-electricity” mode but also offers practical insights for policymakers and agricultural practitioners. By quantifying the benefits of the system and identifying optimal production scales, it contributes to the broader adoption and sustainable development of ecological farming in China. These 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.