The impoundment of the Three Gorges Reservoir (TGR) alters the hydrodynamic conditions and sediment movements related to fluvial sedimentation in the upper stream of the Yangtze River. Based on an extensive dataset of the daily discharge, sediment transport rate, and riverbed level collected from 2003 to 2016 in the TGR area, we applied a Mann-Kendall test, the rescaled range (R/S) analysis method, and 2D numerical modeling to investigate the controls of the temporal-spatial reservoir sedimentation process and their changing trends. The results indicate that (1) the decreasing trends of annual runoff in the upstream of the Yangtze River and its main tributaries are insignificant, and a rapid decrease is not likely to occur, (2) the turning points of the temporal variations in the annual runoff-sediment discharge of the TGR were in 1991 and 2002, (3) the response of the channel pattern to the reservoir sedimentation can be a main factor in controlling the spatial distribution of sedimentation, and (4) an adjustment of the reservoir pool-level can directly influence the sediment processing in the TGR. In the future, dam constructions on the main stem of the Yangtze River and its major tributaries will further decrease the sediment discharge and alleviate sedimentation in the TGR.