Assessment of biodiversity and ecosystem services can provide important base for ecosystem management and decision making. Indicator systems are major tools for scientific assessments. However, no unified indicator systems and methods have been developed for evaluation of biodiversity and ecosystem services in China. It brings poor comparability of evaluation results among different regions and some difficulty in regional and national integration studies. Therefore, it is urgent to establish a scientific, systematic, standard indicator system for evaluation of biodiversity and ecosystem services in China at present. In this paper, we propose the principles of establishing evaluation indicator system, and establish an indicator system for biodiversity and ecosystem services evaluation in China on the basis of the main research outcome in biodiversity and ecosystem services and the cascade relations of biodiversity-ecosystem structure-process and function-ecosystem services.