The Han River-to-Wei River Water Transfer (HWWT) Project not only brings evident economic benefits to the water-receiving areas but it also generates ecological flow value (EFV) by indirectly supplementing river flows. However, the EFV resulting from water transfer is often overlooked due to its indirect nature, and traditional methods tend to overestimate it due to a lack of consideration of value growth thresholds. This paper proposes a research system to address these issues, scientifically quantifying the EFV increment after water transfer. Taking the Xianyang-Lintong river segment in the water-receiving area of the HWWT as an example, we present a holistic approach guided by river ecological issues to determine the suitable ecological flow (SEF) for the river, using it as the growth threshold for EFV. Subsequently, based on water resource allocation, changes in river flow and their relative percentages to SEF (SEF satisfaction) before and after water transfer were analyzed. Finally, an ecological value model based on SEF was employed to estimate changes in river EFV. The results indicate that the distribution of SEF varied throughout the year, correlating with the monthly water requirements of key ecological functions in the river. After water transfer, SEF satisfaction notably improved across all months except excessively wet periods. In drier years, river EFV increased significantly, reaching 31.31% at 95% flow frequency. The water purification, hydrologic cycle, sediment transport and biological diversity, contributed the most to EFV. This study provided new insights and methodologies for assessing EFV increments and formulating ecological compensation standards in the water-receiving areas after water transfer.