In recent decades, the ecohydrology discipline was developed to provide theoretical and technical foundations for the protection and restoration of complex ecological systems (e.g., mountains, rivers, forests, farmlands, and lakes), and to further ecological civilization construction and green development in China. In this study, the progress and challenges of the ecohydrology discipline are elaborated, and the future development directions are proposed according to international scientific frontiers and national ecological civilization construction demands. Overall, the main discipline directions are to develop new ecohydrological monitoring methods, to comprehensively understand ecohydrological mechanisms and their basic theories, to promote integration of multi-scale and multi-variable models by considering both terrestrial and aquatic ecosystems, and to encourage multidisciplinary integration, particularly with the social sciences. Furthermore, the future research interests in China include: combining multi-source information, constructing comprehensive monitoring systems, studying spatiotemporal patterns of key ecohydrological variables and their variation characteristics, developing integrated models of ecological, hydrological, and economic processes, estimating their uncertainty; and conducting interdisciplinary studies that include the natural and social sciences. The application prospects in China are further explored for a variety of ecosystems, including forests, grasslands, rivers, lakes, wetlands, farmlands, and cities. This study will provide a reference to support the development of the ecohydrology discipline in China, and will provide a solid theoretical and technical foundation for the implementation of national ecological civilization construction.