In 2003, Loreau, Mouquet, and Holt from France proposed the meta-ecosystem concept as a natural extension of the meta-population and meta-community concepts. A meta-ecosystem is defined as a set of ecosystems connected by spatial flows of energy, materials, and organisms across ecosystem boundaries. This concept provides a useful theoretical framework toward better understanding and exploring the structures, processes, functions, and heterogeneity of ecosystems. In this paper, we initially introduce the backgrounds of the meta-ecosystem concept, then, describe the development of meta-ecosystem studies, recapitulate the understandings of the meta-ecosystem concept in the current literature, summarize the frameworks for understanding the structure of meta-ecosystems, construct a six-dimensional general framework for describing a meta-ecosystem study, delineate two approaches to studying meta-ecosystems, and describe three spatial structures in empirical meta-ecosystems and two methods for constructing empirical meta-ecosystems. Finally, we explore the frameworks from a meta-ecosystem perspective, that might help future studies of integrated watershed ecosystems. We hope that 1) the review on meta-ecosystems could provide an overall framework for understanding the meta-ecosystem concept and meta-ecosystem studies, and then promote studies using the meta-ecosystem concept and theory; and 2) combining the meta-ecosystem theory and an integrated watershed ecosystem framework could provide a useful conceptual framework for watershed ecosystem studies and watershed ecology, and then support the sustainable development and ecological civilization at the watershed scale.