Abstract: As an important source of biofertilizer, green manure is crucial for soil improvement and sustainable development in ecological farms. However, its effectiveness is influenced by multiple factors and involves trade-offs. Consequently, how to optimize its utilization to maximize comprehensive benefits presents a significant technical challenge for ecological farms. This paper aims to systematically evaluate the integrated benefits of green manure, identify its efficient utilization models, and propose strategies for its optimal application in ecological farms. This study used the literature review method to systematically integrate research findings on the ecological benefits of green manure. Concurrently, a case study of the national-level ecological farm “Zhongde Eco-Farm” was conducted to analyze the practical application models and outcomes of green manure in a real-world production setting. Result indicates that incorporating green manure into the soil significantly improves its properties, leading to an average increase of 13.8% in subsequent crop yields. It also benefits carbon sequestration, increasing soil organic carbon by an average of 17.3%. However, its application involves trade-offs, such as soil moisture depletion and increase in greenhouse gas emissions. The primary utilization models for green manure are rotation and intercropping. Intercropping is commonly practiced in economic crop systems like orchards and tea plantations, while rotation is mainly used for field crops such as wheat and rice. The case of the “Zhongde Eco-Farm” demonstrates that by rationally planning green manure rotation in paddy fields and greenhouses and scientifically selecting green manure species, it is possible to enhance soil fertility while simultaneously considering ecological landscapes and biodiversity conservation. This study reveals the key benefits and trade-offs of green manure application, and refines a set of application strategies: selecting species based on local conditions, rationally arranging planting and management measures, and synergizing with other ecological practices. The findings provide a significant theoretical basis and practical reference for ecological farms to utilize green manure efficiently and rationally, thereby unifying production and ecological benefits.