Over coal mining catchments, reduced or interrupted river flow is particularly prominent, significantly impacting regional economic development and the environment. However, the impact of coal mining on the characteristics of ecological flows, which is of paramount importance for ensuring the catchment ecosystem sustainability, remains elusive. This study utilized the SIMHYD-PML model (a coupled framework that combines the simulation of hydrology (SIMHYD) and Penman-Monteith-Leuning (PML) models) that incorporates groundwater seepage to assess the impact of coal mining on ecological flow in the Huangfuchuan and Gushanchuan catchments located in the Loess Plateau, where intensive coal mining occured. The results revealed that coal mining caused a reduction of similar to 40% in the runoff volume and a downward shift in the flow duration curve in both catchments. Besides, after the coal mining, there was a strong decrease in the frequency and the intensity of high-flow events, while the low-flow event frequency and intensity markedly increased, resulting in an increase in ecological deficit but a decrease in ecological surplus. Specifically, the occurrence of high-flow events in the Huangfuchuan and Gushanchuan has decreased from 1825 to 410, and 1825 to 119, respectively, while the number of low-flow events increased from 2190 to 5169, and 2190 to 6864, respectively. With the increase in coal mining, both the quantity and magnitude of ecological surplus gradually decrease, while those of ecological deficit steadily increase. The ecological health statuses of both catchments were relatively poor and tended to further deteriorate. Specifically, the change in the hydrological indicator due to coal mining activities was moderate (40.2%) in the Huangfuchuan, but became somewhat severe (75.2%) in the Gushanchuan. This study enhances our understanding of the impacts of coal mining on ecological flow, which provides guidelines for sustainable water resources management and utilization of coal resources.