Storage and runoff are the two fundamental surface hydrological variables of a catchment. Research studies have been focused on the storage-runoff (S-R) hysteretic relationship of a catchment and its explanation very recently, thanks to satellite gravimetry. However, a complete analysis of a hydrological process starting from recharge to runoff has not been investigated. The S-R hysteretic relationship of Yangtze River Source Region (YRSR) situated in the northeast Tibetan Plateau is also unexplored. This study aims to investigate the Recharge-Storage-Runoff relationship of this catchment using gravimetrically-derived terrestrial water storage (TWS), satellite-derived and gauged precipitation, land surface modeled and gauged evapotranspiration, and runoff data measured during 2003–2012. We found that the Pearson correlation coefficient (PCC) of S-R relationship is 0.7070, in addition to the fact that the peak of runoff every year comes earlier than that of the storage. This finding enables us to further calculate equivalent runoff based on water balance equation using the above data, while comparing to measured runoff time series. The comparison of Global Land Data Assimilation System (GLDAS)-derived (gauge-derived) equivalent runoff against measured runoff reveals a PCC of 0.8992 (0.9402), respectively, indicating both storage and runoff are largely controlled by the recharge derived from precipitation and evapotranspiration. This implies the storage is not coupled with runoff prominently due to steep topography in YRSR unable to hold the water in the form of storage. Exceptional anomalous water storage time series in 2006 has also been investigated. We speculate that the low rainfall might partly be related to an El Niño Southern Oscillation event. The low rainfall and abrupt groundwater transfer are likely to be the causes of the anomaly in 2006.