Based on a brief introduction of the previous theoretical system of human-water relationship, the branches of human-water relationship discipline were introduced. The basic principles of human-water relationship discipline were summarized and proposed, including the interaction principle of human-water relationship, the self-adaptive principle of human-water system, the balance transfer principle of human-water system, and the harmonious evolution principle of human-water relationship. The theoretical system of human-water relationship, including theoretical basis and basic theories, is discussed. The theoretical basis includes hydrology, water resources, water environment, water security, economics, sociology, etc. The basic theories include human-water system theory, human-water cybernetics, human-water harmony theory, human-water game theory, human-water synergy theory, water crisis and conflict theory, human-water relationship dialectic theory, human-water relationship sustainable development theory, etc. The application prospect of the basic theories was also analyzed.