Abstract: Agroecology has emerged as a key pathway to achieve the dual goals of agricultural sustainability and ecological environmental protection. However, their development has been hindered by conflicts between short-term private economic interests and long-term public ecological benefits. Eco-compensation has emerged as a vital economic tool for bridging this gap and incentivizing sustainable practices in agriculture. A methodology for calculating agricultural eco-compensation standards is essential for establishing a reasonable eco-compensation mechanism. The key scientific issue currently impeding the effective execution of agricultural eco-compensation is the ineffective identification and valuation of agricultural ecosystem services. These services are difficult to quantify economically, and lead to incomplete accounting systems. Moreover, current approaches often fail to integrate ecosystem service values (positive contributions from ecosystems) with ecosystem disservice values (negative contributions from ecosystems). The lack of a comprehensive accounting framework has resulted in compensation schemes that do not fully reflect the actual ecological and economic dynamics of agricultural systems. Consequently, establishing a structured method for determining agricultural eco-compensation standards considering ecosystem service and disservice values to enhance the implementation of agricultural eco-compensation strategies and steer agro-ecosystem management, is important. This paper proposes a comprehensive framework for implementing and managing agricultural eco-compensation. The framework addresses the full scope of economic costs and benefits by considering the complex interplay between ecosystem services. Indicator systems and monetization methods were elaborated for these values, offering theoretical support and methodological guidance for determining eco-compensation standards. This study also discusses economic costs, relative ecological values, and a scenario analysis of agricultural eco-compensation to provide references for setting reasonable eco-compensation standards across various regions. This study identifies several promising directions for future research. First, comprehensive life cycle assessments (LCA) of agricultural ecosystem service values should be used, which can provide a more complete understanding of the long-term benefits and costs associated with different agricultural practices and help refine compensation standards. Another important research area is the development of region-specific eco-compensation strategies because of the different performances of socioeconomic development and operational levels of farmers. This study advocates the integration of academic research with practical applications to ensure that advances in agricultural eco-compensation theory can be effectively translated into policy and practice. By addressing these issues, agricultural eco-compensation can play a pivotal role in promoting the coordinated development of agricultural sustainability and ecological protection. A well-designed eco-compensation standard not only encourages farmers to adopt sustainable practices but also ensures that they are fairly compensated for the ecological services they provide, aligning economic incentives with long-term environmental goals. These prospects are expected to support the formulation and implementation of agricultural eco-compensation policies and promote the coordinated development of agricultural sustainability and eco-environmental protection.