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Climatic warming has resulted in permafrost degradation and it is expected to alter the hydrological processes and hydraulic connectivity on the Qinghai-Tibet Plateau (QTP). Some important and pending issues for understanding the hydrological processes in permafrost regions are how much melting water from thawing permafrost can feed the stream water and how the hydraulic connectivities will be altered under continual permafrost degradation. In this study, the Source Area of the Yellow River locating on the Northeast QTP was studied by using stable isotopic method and field hydrological observation. Results exhibited significant seasonal hydrological variations of stream water, thermokarst lakes, and ground ice. Hydrograph separation suggested that precipitation is the main contributor to stream water in ice-free months, accounting for 53.5% and 52.2% of the streams on average for the two branches, respectively. The second source is springs, which contributed about 29.8% and 17.9%. However, the recharge from melting ice is also important; it exported an average of 16.7% and 13.2% to the surface stream. Conceptual model and stable isotopes emphasized the remarkable hydraulic connectivities between the precipitation, stream water, thermokarst lakes, spring, and the near-surface ground ice. Current findings provide a basic understanding of the log-term hydrological processes under permafrost degradation, and can offer an efficient way to assess future hydrological changes and water resource protection.