Facing the increasingly serious water shortage problem, with the increasing demand for water resources, the development and utilization of rivers by human beings have been enhanced, which significantly changed the natural hydrological process of basins. The basic ecological water demand of rivers cannot be guaranteed, and the shortage of ecological water supply has become an important factor restricting the health of watershed ecosystem. In order to effectively guarantee the river ecological flow, the Soil and Water Assessment Tool (SWAT) model was used to simulate the natural runoff and the current runoff process with inter basin water transfer in Fenhe River Basin of Shanxi Province based on the natural and measured hydrological data. First, based on the SWAT model, the monthly natural runoff for about 30 years and the monthly current runoff after the implementation of inter basin water transfer projects in recent 10 years were simulated in the Fenhe River Basin. Second, based on the improved Tennant method, the ecological flow values under different ecological flow criteria were quantified in each river channel in flood season and non-flood season. Last, the temporal and spatial distribution characteristics of ecological flow and ecological water shortage were analyzed in the whole basin. The results showed that:(1) the ecological flow of each channel showed significantly temporal and spatial differences, with the values were 0.05-1.81 m3/s for non-flood season and 0.50-18.8 m3/s for flood season. The overall distribution characteristics were that the ecological flow in the middle and lower reaches was much higher than that in the upstream tributaries. (2) Under different ecological flow criteria of Tennant method, the satisfaction of ecological flow in non-flood season was better than that in flood season, and the areas with high-frequency of water shortage were mainly distributed in the upstream and downstream tributaries. (3) Under the medium-level environmental flow standards, about 84% of the basin could guarantee the basic ecological flow demand, and the key water shortage areas were Lanhe, Xiaohe, Fushan County and Huihe River basin. (4) The ecological water supplement of the basin should focus on flood season in time and areas with high frequency of water shortage in space, and the water resources of inter-basin water transfer projects should be allocated based on the spatial and temporal distribution characteristics of ecological water deficiency to improve the utilization efficiency of water. In conclusion, this study quantified the satisfaction degree of ecological flow after the implementation of inter basin water transfer projects in time and space, which can provide effective guidance for watershed water resources management.