As the Regional Hydro-Ecological Simulation System (RHESSys) is a tool to simulate the interactions between ecological and hydrological processes, many RHESSys-based studies have been implemented for sustainable watershed management. However, it is crucial to review a RHESSys updating history, pros, and cons for further improving the RHESSys and promoting ecohydrological studies. This paper reviewed the progress of ecohydrological studies employing RHESSys by a bibliometric analysis that quantitatively analyzed the characteristics of relevant studies. In addition, we addressed the main application progress, parameter calibration and validation methods, and uncertainty analysis. We found that since its release in 1993, RHESSys has been widely applied for basins (<100 km2) within mainly seven biomes. The RHESSys model has been applied for evaluating the ecohydrological responses to climate change, land management, urbanization, and disturbances, as well as water quality and biogeochemical cycle. While most studies have paid their attention on climate change, the focus has shifted to the application for land management in recent years. This study also identified many challenges in RHESSys such as the inaccessible data and parameters, oversimplified calibration approach, few applications for large-scale watersheds, and limited application fields. Therefore, this study proposed a set of suggestions to overcome the limitations and challenges: (1) Developing a new approach for parameter acquisition and calibration from multi-source data, (2) improving the applicability for a large-scale basin, and (3) extending the scope of application fields. We believe RHESSys can improve the understandings of human–environment relationships and the promotion of sustainable watersheds development.