This paper presents an analytical framework of Conceptual Understandings of Earth Systems (CUES) that shows a relationship between disciplinary knowledge of Earth systems and the specific thinking skills required to understand that knowledge. This framework is developed through an extensive literature review of students’ and teachers’ understandings of earth systems concepts and systems thinking in earth science context. This study first presents the categories of disciplinary knowledge of Earth systems, Earth System Knowledge (ESK). This study then illustrates a relationship between categories of ESK and the ontological categories (Matter, Process, Systems) that has been used to study students’ conceptual understandings of Earth systems. Finally, this study presents the CUES framework to show the relationship between disciplinary knowledge and thinking skills. The implications of using this framework for curriculum development, assessment, and teacher education and ESS research are discussed.