With increasing numbers and types of nature reserves (NRs), objective evaluation and comparison of the effects of different nature NRs on conservation efforts are of great importance for protecting species diversity, ensuring reasonable national economic input, and adjusting government management schemes. Developing a method for the combined assessment of flagship or umbrella species and ecosystem quality will improve the evaluation of NRs. However, it is also important to establish a new framework for rapid evaluation of ecosystem quality, supported by the advantages of scientific, economic, and regular principles. Here, we proposed a new framework that incorporates the novel concept of ideal references into evaluation systems, which will facilitate the comparison of results from different periods and regions. Furthermore, from the perspective of making the framework as objective, rapid, and economical as possible, we recommended some key ecological indicators, such as net primary productivity, soil organic matter, plant diversity, for use in the new evaluation framework. The new framework, referred to as “ideal reference and key indicators” (IRKI), can sufficiently meet the requirements for the rapid evaluation of ecosystem quality both regionally and nationally. Furthermore, IRKI can identify the restoration potential and restoration periods of NRs, thus facilitating the rational distribution of resources and enhancing the protective effect. There are many types of NRs in China, and it is necessary to partially alter the assessment methods or parameters for different types of NRs. Overall, IRKI provides a simple, clear, and comparable framework that will strongly enhance the conservation of protected areas (PAs) and facilitate the standardization of management practices.