Water resource is a limiting factor of economic and social development. The overexploitation and utilization of water resources have significantly affected ecological protection and high-quality development in a region. Ecological flow has been treated as an effective and critical index to ensure the sustainable development and management of the ecological environment in a basin. Thus far, numerous research frameworks and methods have been developed and applied across the globe. Yet, they have not been systematically reviewed and compared in China. This paper summarized the latest progress in domestic ecological flow assessment and systematically compared and summarized 17 ecological flow methods within four categories, including the hydrology method, hydraulic rating, habitat simulation modelling, and holistic frameworks. We reviewed their advantages and disadvantages, and their prerequisite for practical application. Based on the current situation of ecological flow assessment in domestic river basins in China, we suggested that the ecological flow assessment method should be selected based on local conditions when the water system was under complex climate, hydrogeology, underlying surface, and water utilization and allocation. Future ecological flow research and watershed water ecological management should comprehensively consider the influences of climate, hydrological conditions, and human activities to improve watershed management and research. To achieve sustainable and high-quality development of water resources, water conservancy, hydropower engineering scheduling, ecological flow monitoring, watershed system and regulations construction should be fully considered in setting the ecological flow of a watershed.