FJS (Fujiangsha) section of the Yangtze estuary with braided shoals distributed in the channel, is a complicated and bifurcated plain river. River bed nearby, impacted by runoff and current flows, is divided at the wide river sections. The main passage is bifurcated and the 12.5 m deep contour breaks at many navigation sections. So FJS section becomes an obstructed river for vessels sailing. The Ministry of Transport intends to implement construction of 12.5 m deep-water navigation channel under Nanjing during the “Twelfth Five-Year Plan” period. The principle of the control project is “Following river evolution; Keeping originally as bifurcated; Protecting SJS (Shuangjiansha) shoal; Stabilizing the navigation channel”. Based on the measured data, we analyze the river regime evolution. The results show that: 1) With the cyclical change of the hydrological year, sand bodies and inlets will be replaced by each other over and over again which has negative impact on the navigation stability so that there is great necessity of SJS shoal protection project; 2) Due to the restriction of shore lines, navigation channels in Fubei and Funan waters stay stable, besides, the depth can be deepen to 12.5 m contour by dredging measures while the width of the passage cannot be guaranteed; 3) According to the river regime evolution, Fuzhong passage, with a wide main channel and a moderate turning curvature, has a trend of erosion which is to make a better navigation condition.