Xi Jinping’s thought on water governance and his important statements on water governance are the action guide of our country’s water governance work in the new era. Taking systematic governance as the starting point, this paper delves into the systematic philosophical foundation of water governance thinking from the perspectives of ontology, epistemology, and methodology, with the aim of deepening its theoretical connotation and providing a scientific methodology. Human and water as a community of shared destiny is the ontological foundation of Xi Jinping’s thought on water governance, in accordance with the principles of integrity, hierarchy and openness of the system. The harmonious coexistence of human and water is the main thread of Xi Jinping’s systemic epistemology on water governance, explained from three aspects: respecting nature, following nature’s ways and protecting nature. Focusing on the systematic, integrated, and coordinated nature of water governance is the methodological guidance of Xi Jinping’s thought on water governance. The approaches of system analysis, system synergy and system engineering are used to explore the practical path.