Ecohydrology is a key discipline developed in recent decades, which can give aid in the protection and restoration of complex ecological systems (e.g., mountain, river, forest, farmland, lake), ultimately promoting the ecological civilization construction and the green development of China. In this paper, the progress and existing challenges of ecohydrological discipline are elaborated, and the future development directions are proposed according to the international scientific frontiers and national demands on ecological civilization construction. The main directions are to develop new ecohydrological monitoring methods and improve comprehensive observation network of ecohydrological systems; to perfect the ecohydrological mechanisms and their basic theories; to promote the integrations of multi-scales and multi-elements by considering both terrestrial and aquatic ecosystems; to promote the multidisciplinary integrations between ecohydrology and social sciences. Furthermore, specific future research interests in China are proposed as follows: multi-source information fusion and comprehensive monitoring system construction, spatio-temporal patterns of key ecohydrological elements and their variation characteristics; integrated models of ecological, hydrological and economic processes and their uncertainty estimation; interdisciplinary studies including physical and social sciences. The application prospective in China is further explicated in a variety of ecosystems (e.g., forest, grassland, river and lake, wetland, farmland and urban area). This paper is expected to provide a reference to support the development strategy of the ecohydrological discipline in China, and to give a theoretical foundation and technical support for the implementation of national ecological civilization construction.