To enhance the understanding of the integrity and complexity of watershed systems and the challenges they face, based on the connections among the five major units, i.e., the headwaters, upper reaches, middle reaches, lower reaches, and estuary, in terms of hydrology and sediment transport, topography and geomorphology, nutrients, and ecological elements, the integrity of watershed systems was elucidated from the perspective of the cascading relationships between physical and human geographical characteristics of the five units. Based on the characteristics of the interaction mechanisms among internal elements and subsystems, the inherent contradictions underlying the complexity and difficulty of watershed system governance were analyzed. From the geoscience perspective, the external influences on watershed system governance by the atmosphere, hydrosphere, lithosphere, anthroposphere, and biosphere were examined based on interactions among the Earth’s sphere interactions. Finally, the constraints to the sustainable operation of watershed systems in the context of “Anthropocene” were summarized, including climate change, technological development, policies and regulations, and the international situation. Considering the integrity of the watershed system and the challenges arising from both internal and external factors, key research directions were proposed to ensure the sustainable operation of watershed systems. These directions include establishing a theoretical framework for sustainable watershed system operation based on the cascading relationships among five units, identifying the critical thresholds governing regime shifts in the relationships among watershed system elements and subsystems, and developing a watershed system simulator that integrates holistic and reductionist approaches. Keywords: geoscience perspective; integrity of watershed system; watershed system governance; sustainable development of watershed 〖FL