The operation of the Three Gorges Project has significantly altered the flow and sediment conditions, causing long space-time scale erosion and deposition adjustment downstream the dam. Analysis of the equilibrium sediment transport in the middle and lower reaches of the Yangtze River is an important basis for rationally evaluating the impact of the dam construction, and also a key support for the management and protection of rivers and lakes. Based on long-term series of observation data, the sediment balance method is used to analyze the sediment recovery characteristics in the middle and lower reaches of the Yangtze River. Comparing with the section topographical method, the reasons for the two different calculated results of scouring-silting amount are revealed from several factors including the error of the bottom suspension test, the cross-section representativeness or interval distances, and sand mining. The results show: (1) From 2003 to 2018, the Yichang-Datong reaches has scoured 10.76 billion tons of sediment, of which the erosion volume of the particles d<0.125 mm accounted for 90.9%. Taking Luoshan as the boundary, the river section from Yichang to Luoshan presents as “coarse and fine sediment scouring”, and the section between Luoshan and Datong is “fine sediment scouring and coarse sediment silting”; (2) The relative deviation of the calculated erosion and silting amount between sediment balance method and the section topographical method from Yichang to Datong in 2003-2018 is 71%. Longitudinal distribution of the absolute differences calculated by the two methods indicates that from Yichang to Shashi which is closer to the dam is smaller, while the river section from Shashi to Datong is relatively larger, accounting for nearly 86% of the absolute deviation of the entire reach from Yichang to Datong; (3) The amount of sand mining from Yichang to Shashi accounts for about 20% of the measured erosion, while the correction ratio of bottom suspended sediment transport is from 13.2% to 26.7% (average about 20%). After correction, the two calculation results are relatively fit. However, the main reasons for the calculated differences from Shashi to Datong include sediment test, fixed section layout, and sand mining.