Evaluating, simulating, and predicting the status and trends of biodiversity and ecosystem services, as well as their impacts on human well-being, are currently the primary goals for researchers in the field of biodiversity and ecosystem services, and indicators and data models and scenarios are major tools for the theoretical and methodological integration of biodiversity and ecosystem services. However, few detailed studies have conducted comprehensive analyses or comparisons of indicator systems or reported methods for evaluating biodiversity and ecosystem services. In this paper, we review recent work regarding the conceptual framework, indicator systems, and various types of models and methods related to the assessment of biodiversity and ecosystem services. The biodiversity-ecosystem function-services-human well-being cascade model is a more expressive logical framework, and owing to various problems and challenges, existing indicator systems and methods are ineffective for elucidating the mechanisms that determine the formation and impact of ecosystem services, for identifying internal connection and function mechanisms among services, or for offering guidance for ecosystem service management and policy making. However, existing indicator systems and methods provide an important entry point for constructing a synthetic evaluation model. Through a comprehensive analysis and comparison of current indicator systems and methods, we propose several core elements for studies of synthetic evaluation models, including i) Objectives, determining the scientific problems and developing schemes for ecosystem services management and decision making by scenario analysis based on the fundamental characters of interactions between nature and society; ii) Content, the comprehensive analysis of scales, service types, hierarchical nature of biodiversity, relationship among the components, drivers, and multi-source data; and iii) Methods, conducting comparison and uncertainty analyses of various types of models and model combinations, in order to establish a comprehensive map-making model base system that is suited for regional analyses. Accordingly, we propose that China should develop a standard indicator system and a synthetic evaluation model of biodiversity and ecosystem services that is suited to the nation's regional characteristics as soon as possible, in order to periodically evaluate, simulate, and predict the status and trends of biodiversity and ecosystem services and to enhance China's position and power of discourse in the international arena of this field.