Storm runoff in headwater catchments on the Chinese Loess Plateau has been significantly impacted by afforestation. Monitoring rainfall, soil moisture, and streamflow in grass and forest catchments revealed that afforestation reduced storm runoff by ten times. Peak rainfall intensity controlled runoff in grasslands, while forestlands were less affected. Specific thresholds for soil moisture and rainfall were identified in grasslands, leading to increased runoff. Overall, long-term afforestation changed storm runoff mechanisms and patterns, highlighting the importance of rainfall intensity, amount, and soil moisture in determining hydrological connectivity in catchments.