The flow and sediment condition in the middle and lower reaches of Yangtze River (MLYR) was changed a lot after the impoundment of Three Gorges Reservoir (TGR), and further, the evolution process of the sandbars and shoals were affected, both of which have obvious influence on the navigation in the MLYR. Based on the field data, the analysis shows that the changes of flow and sediment favored the waterway condition, which includes the elevation of the lowest water level, the extension of the scour time of shoals, the increase of the erosion speed of shoals caused by the reductive sediment. After the operation of TGR, the frequency of the bank collapse and the sandbar cutting is increasing, and the shoal tends to shrink. However, not all the deformation of sandbars and shoals will obstruct the waterway, only the Critical Width of Returning to Channel (CWRC) is more than the critical river width, the channel will not be unimpeded. The CWRC is about 900–1900m, varying with the navigation base surface and the channel dimension.