Influenced by climate change and human activities, especially the completion and operation of cascade reservoirs in the middle and lower reaches of Jinsha River since 2012, new changes have taken place in the water and sediment characteristics of the Three Gorges Reservoir (TGR) in recent years. In this paper, a one-dimensional unsteady water and sediment mathematical model of the main and tributary rivers of the TGR is established, and the main calculation parameters of the model are calibrated with the measured water and sediment data from January 1, 2008 to December 31, 2017. In view of the different combinations of inflow water and sediment that may occur in the TGR under the condition of new water and sediment, the long-term changes of sediment erosion and deposition and the balance of reservoir deposition in the TGR are studied using the model. The results show that: (1) Under the new conditions of water and sediment, the amount of sediment in the TGR accounts for only 14.8% and 35.8% of that in 1956–1990 and 2003–2012, respectively; (2) The variation process of water level, discharge and sediment concentration of each station along the route calculated by the model is basically consistent with the measured results, and the calculated values of total deposition amount and deposition distribution are also basically consistent with the measured results. The verification results of the model are in accordance with the measured values; (3) Under the water-sediment conditions during 1961–1970 and 1991–2000, the model predicted the estimates of 320 and 430 years for the TGR to reach a sedimentation balance, respectively. Under the new water-sediment conditions, it takes 560 years at most and 450 years at least to reach the sedimentation balance for the TGR, and the corresponding condition is the typical year with less water-less sediment and more water-more sediment, respectively. The research results of this paper can provide a new reference for the long-term safe operation and operation optimization of the TGR.