Since the early 21st century, the Yellow River Source Basin (YRSB) has faced multiple flow disruptions, threatening water security for nearly one million downstream residents. Efforts such as the Ngoring Reservoir and Sanjiangyuan Ecological Reserve initially mitigated these issues. However, global climate change and the decommissioning of the Ngoring Reservoir have renewed these concerns. This study integrates multi-source satellite data (altimetry and imaging) and in-situ measurements (station and field) to simulate runoff in the YRSB from 2000 to 2020 and predict it with the IPCC data from 2021 to 2070 by long short-term memory (LSTM) model. Calculation results indicate that from 2000-2020, water storage in Lake Gyaring and Lake Ngoring increased by 0.47 billion m³ and 0.65 billion m³, respectively, with soil water rising by approximately 0.60 billion m³. About 40% of Lake Ngoring’s water comes from Lake Gyaring, crucial for mitigating extreme events if ecological integrity is maintained. Simulation runoff in high temperature is more sensitive to precipitation changes, while runoff in low temperature is more affected by evapotranspiration. Prediction results shows that under the most probable future, SSP 370 scenario, runoff recharge is expected to increase until mid-century but decline significantly thereafter due to rising evaporation, when the YRSB may be at risk of breakage.