Generally, the high levels of biodiversity found in natural ecosystems have positive effects on ecosystem functions (EFs), though the intensity and direction of such effects can vary. This is associated with the impacts of other EF-driving factors. In this study, the factors that affect biodiversity-ecosystem functioning (BEF) are reviewed and summarized, and current gaps in the research on the effects of these factors on BEF are discussed. Moreover, a new conceptual model, the generating-presentation model, accounting for links between effect factors and EFs, is built to provide a systematic means of understanding how different factors affect BEF. The model shows that the correlation between biodiversity and EFs can be described as involving a cascade process, while the separation of biodiversity and EFs from ecosystems without considering integrated features is not appropriate for BEF-related research. The generating-presentation model can comprehensively reflect the effects of different factors on EFs and thus has major theoretical and applied implications.