Good regulation effects have been achieved for the Phase I and Phase II projects of the 12.5 m deepwater navigation channel from Nanjing. Regarding the problems that the Tongzhou shoal is not completely stable，and the Xinkai shoal is still being scoured and keeps retreating，this study focuses on the subsequent improvement engineering to stabilize the channel and adopts the test scheme of the fixed-bed physical model to study the flow field after the implementation of improvement engineering. The study shows that the hydrodynamic axis of the improvement engineering scheme has a certain degree of northeastward migration at the inlet of the Nantong waterway and eastern Tongzhou shoal waterway. The scheme can greatly reduce the overtopping rising-tide volume of the embankment line of the Tongzhou shoal and the overtopping ebb-tide volume of the erosion ditch between Xinkai shoal and Kuzigang shoal. The average ebb-tide flow velocity in the reach between Tianshenggang and Longzhaoyan generally increases due to the engineering，and the increased range generally covers the existing channel position. The ebb-tide dynamics and the capacity of sediment transport by ebb tides are enhanced. Therefore，the improvement engineering can achieve the desired goal of protecting shoals and improving waterway maintenance conditions.