Abstract: The hyporheic zone (HZ) serves as one of the key areas for watershed ecological restoration. HZ restoration is intended to ensure the flow of energy, material and information between adjacent water systems. The restoration of HZ connectivity depends on hydrological, ecological, and functional connectivity. Studies related to ecological restoration of HZ are mainly based on hydrodynamic, geological and ecological theories. Most of the studies analyze the biogeochemical coupling mechanism driven by HZ. They report ecological restoration technologies that promote HZ exchange and restore biodiversity. The improvement of hydrologic conditions and the recovery of biological species in the HZ are additional goals for the comprehensive restoration of the HZ ecosystem structure and function. Based on the perspective of hydrological, ecological and functional connectivity, this study reviews the theoretical and technological progress in the hydrodynamic features, media properties, biome composition, food web structure and ecological function during the restoration of HZ connectivity. A multi-disciplinary approach is needed to expand the theory and practice of research methods and scales. Multi-omics approaches are suggested for the exploration of ecological processes on a microscale. The mechanism of restoration needs to be elucidated on both temporal and spatial scales. Finally, a framework for ecological restoration of the HZ under various scenarios should be constructed.