In order to reach the goal of extending the deepwater channel to Nanjing，the navigation channel regulation projects were carried out at Fujiangsha waterway by the phaseⅡof 12.5 m deepwater channel project in the Yangtze River below Nanjing. Regulation project is mainly including spur dike at the left edge of Fujiangsha，submerged dike at the head of Shuangjiansha，spur dike at the north side of submerged dike and spur dike at the south side. Based on the measured data after the implementation of the channel regulation project of Fujiangsha waterway，this paper makes a comparative analysis with the predicted results of the digital and physical model in the design stage，and comprehensively analyzes the realization of river regime changes，flow field changes，and channel maintenance volume and other aspects before and after the project. The results show that：1）After the implementation of the project，the scour trend of Shuangjiansha head has been well controlled. So the siltation near the sand head on the upstream side and the spur dike on the north side of the submerged dike is obvious，and the volume of sand body is obviously increased. 2）The scour and siltation in the upper middle section of the left edge of Fujiangsha is relatively stable and generally presents the siltation trend，and there is scour in the lower part. The volume and area of sand body on the left edge of Fujiangsha are generally increased. Remediation project has better effect of bank protection and sand fixation. 3）The overall distributary pattern of Fujiangsha waterway has not changed significantly，only the flow field around the regulation building has been adjusted. 4）The amount of channel maintenance has increased. The project has achieved the expected goal of channel regulation，the project regulation scheme is reasonable，and the effect of channel regulation is in line with the expectation. It can be used as a reference for channel regulation of tidal branches in the middle and lower reaches of the Yangtze River.