In order to analyze the impact of climate change and ecological construction measures such as vegetation and silt dams on runoff changes, the Qingshui River and Kushui River, typical watersheds into the Yellow River in Ningxia, were selected as the research objects. The Pettitt mutation method were used to detect the change points of meteorological, hydrological, and ecological construction measure series, and the multivariate linear regression equations between the land surface parameter and ecological construction measures were constructed, rainfall runoff model coupled ecological construction measures was derived based on the Budyko theory, the applicability of the model was evaluated, and the elastic coefficient method was used to quantify the contribution rate of different ecological construction measures to runoff changes. The results indicated that the runoffs in the study watersheds showed decreasing trends, and the change points of annual runoff occurred around 2000. The land surface parameters had significant positive correlations with the NDVI and silt dam index, and the simulated values from the rainfall-runoff model constructed by the introduction of the NDVI and the silt dam index are close to the observed values. The contribution rate of ecological construction measures to the reduction of runoff was as high as 78.5% in the Qingshui River basin, and vegetation and silt dams contributed 23.11% and 46.50%, respectively. The impact of ecological construction measures on runoff was much greater than that of climate change. The contribution rate of rainfall to runoff reduction in the Kushui River Basin can reach 47.30%, and the contribution rate of ecological construction measures was 59.57%, with vegetation and silt dams contributing 18.57% and 13.96% respectively, while the contribution rate of other ecological construction measures to the reduction of runoff was 27.04%. Ecological construction was the main driving factor causing changes in runoff in the Ningxia Yellow River Basin. The research results can provide theoretical support for optimizing the layout of ecological construction in Ningxia.