Abstract: Agro-ecology emerges as a key pathway to achieve the dual goals of agricultural sustainability and ecological environmental protection. However, its development is hindered by the conflict between short-term private economic interests and long-term public ecological benefits. Eco-compensation has emerged as a vital economic tool to bridge this gap and incentivize more sustainable practices in agriculture. The methodology for calculating agricultural eco-compensation standards is essential for establishing a reasonable eco-compensation mechanism. The key scientific issues currently impeding the effective execution of agricultural eco-compensation are the ineffective identification and valuation of agricultural ecosystem services. The services are difficult to quantify in economic terms, leading to incomplete accounting systems. Moreover, current approaches often fail to integrate both ecosystem service values (the positive contributions of ecosystems) and ecosystem disservice values (the negative contributions of ecosystems). This lack of a comprehensive accounting framework results in compensation schemes that do not fully reflect the true ecological and economic dynamics of agricultural systems. Consequently, it’s important to establish a structured method for determining the agricultural eco-compensation standards, taking into account ecosystem service and disservice values, to enhance the execution of agricultural eco-compensation strategies and steer the agro-ecosystem management. This paper proposes a comprehensive framework for the implementation and management of agricultural eco-compensation. The framework addresses the full scope of economic costs and benefits, taking into consideration the complex interplay between ecosystem services and disservices. The indicator systems and monetization methods was elaborated for these values, offering theoretical support and methodological guidance for determining eco-compensation standards. The paper also discusses ecological conservation costs, relative ecological values, and scenario analysis of agricultural eco-compensation to provide references for setting reasonable eco-compensation standards across various regions. In terms of future research, this paper identified several promising directions. Firstly, the comprehensive life cycle assessments (LCA) of agricultural ecosystem service values should be used, it can provide a more complete understanding of the long-term benefits and costs associated with different agricultural practices, helping to refine compensation standards. Another important research area is the development of region-specific eco-compensation strategies because of the different performance of socio-economic development and the operational level of farmers. The paper advocates for integration of academic research with practical applications, ensuring that advances in agricultural eco-compensation theory are 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, promoting the coordinated development of agricultural sustainability and eco-environmental protection.