Ecological supervision which is comprised of ecological monitoring and management is crucially important for the health and sustainability of the ecosystem. In China, the government has put great efforts into ecological civilization construction to ensure regional ecological security, and finally to achieve sustainable development. To achieve that goal, we urgently need a scientific and effective ecological supervision framework to guide the construction of ecological civilization. Ecological supervision related to multiple dimensions such as social, economic, natural dimensions which directly or indirectly affect the eco-environment, and involves a broad range of elements such as water, soil, atmosphere, biodiversity, etc. which supervised by different government departments, and across many scales from regional ecosystem to local patches which governed by different levels of jurisdictions. Due to the mismatching of ecological processes and social management systems, the supervision of the ecosystem at present is separated in many ways. For example, the supervision of a forest ecosystem was usually separated by administrative boundaries, and the supervision of the trees, water, and atmosphere of the forest were belonging to a different department. The separation of those dimensions, elements, and scales will lead to insufficient information for decision-making. Thus, it is essential to develop a framework to integrate those parts and guide the ecological supervision in a scientific, systematic, and spatial explicit way. Our research developed a hierarchical ecological patch (HEP) framework by integrating the hierarchical patch dynamic paradigm, the social-economic-natural complex ecosystem theory, and multifunctional theory. The hierarchical patch dynamic paradigm provides a holistic scheme to organize different dimensions, elements, and scales. The hierarchical patch dynamic paradigm considers the ecosystem as a nested structure comprised of patches, providing spatial explicit objects for supervision. In addition, the hierarchical structure of the patches enables supervision in and across different scales. The social-economic-natural complex ecosystem theory provides a comprehensive view to understand the patches. In the past, the patches in the hierarchical patch dynamic paradigm merely represented biologically related features. In the HEP framework, however, each patch in all scales must also consider social and economic features, which are the key information to bridge the ecological process and the social management system. With the multifunctional theory, each dimension of a patch can be further divided into specific functions, which is crucial for making corresponding monitoring and supervising strategies. Therefore, the HEP framework we developed here is expected to realize the scientific, systematic, and spatial explicit ecological supervision and eventually support the construction of ecological civilization.