Deep hydrogeology has emerged as a frontier field of research in the earth sciences, focusing on bedrock fracture aquifer systems at depths ranging from hundreds to thousands of meters. As China’s demands for deep resource development, environmental protection, and subsurface space utilization continue to grow, understanding and managing deep groundwater systems have become key scientific and technological challenges that support national strategic goals. This paper systematically reviews the research progress in deep hydrogeology, with an emphasis on key scientific issues, research methodologies, and engineering practices related to fluid flow in deep fractured media. First, it identifies five core scientific issues: the origin and age of deep groundwater, the mechanisms of interaction between deep and shallow hydrological cycles, the characterization of highly heterogeneous aquifer systems, the interactions between deep fluids and engineering projects, and the influence of the deep biosphere. Second, it systematically reviews key methods and technologies for investigating fluid flow and transport in deep fractured media, including high-precision laboratory observation and testing techniques, field experimentation and long-term monitoring approaches, multi-scale numerical simulation and multi-field coupling modeling technologies, as well as multidisciplinary integration and artificial intelligence research paradigms. Third, within typical engineering contexts, the paper discusses research advances related to four types of deep hydrogeological challenges: (1) fluid flow in deep low-permeability fractured rocks, using the geological disposal of high-level radioactive waste as an example, to analyze the characteristics of deep groundwater systems and hydrological circulation patterns in the pre-selected Beishan area; (2) solute transport in deep low-permeability fractured rocks, using shale gas hydraulic fracturing as an example, to explore the hydrogeological controls on the upward migration of deep fluids; (3) reactive transport of deep fluids, using deep carbonate reservoir space as an example, to reveal the dominant role of deep hydrothermal fluids in reservoir modification; and (4) Coupled thermo-hydrological processes in deep fractures, using the development of Enhanced Geothermal Systems as a case study, to analyze the governing mechanisms for reservoir fracture evolution and the sustainability of heat extraction under multi-physics coupling. Finally, the paper outlines six future research directions, including the systematic development of deep observation technologies, high-precision modeling of fracture flow, enhancement of multi-field coupling simulation capabilities, the integration of geophysical imaging with hydrogeology, high-resolution hydrochemical analysis, and the integration of artificial intelligence with big data analytics. This comprehensive summary of the theories, methods, and applications of deep hydrogeology aims to provide theoretical guidance and technical support for deep geological engineering projects such as the geological disposal of high-level radioactive waste, shale gas development, geological carbon sequestration, enhanced geothermal systems, and the exploitation of deep and ultra-deep oil and gas resources. This review also aims to provide a scientific basis for the sustainable management and environmental safety assessment of deep groundwater resources.