By comparing the original particle gradation of sediment from the Three Gorges Reservoir with the single particle gradation, the differences in these two particle gradations showed that there is sediment flocculation in the Three Gorges Reservoir, which can accelerate the sediment deposition rate in the reservoir. In order to determine the influence of flocculation on the sediment settling velocity, sediment was collected at the Three Gorges Reservoir, and the indoor quiescent settling experiment was performed to study the mechanism of sediment flocculation. The experimental results showed that sediments aggregated from single particles into floccules in the settling processes. The single particles smaller than 0.022 mm will participate in the formation of floccules, which accounts for 83% of the total amount of sediment in the Three Gorges Reservoir. Moreover, the degree of sediment flocculation and the increase in sediment settling velocity were directly proportional to the sediment concentration. Taking the average particle size and the median particle size as the representative particle size, respectively, the maximum flocculation factors were calculated to be 3.4 and 5.0. Due to the sediment flocculation, the volume of sediment deposition will increase by 66% when the mass settling flux factor of total sediment had a maximum value of 1.66, suggesting that flocculation has a significant influence on the sediment deposition rate in the Three Gorges Reservoir.