Tongzhou shoal channel in Chengtong Reach of the lower Yangtze River is a typical bifurcation channel with multiple shoals as well as complex and variable river regime and waterway condition under combined riverine and tidal forcing. After river and waterway regulation projects in recent years, the flooding and ebb currents converged along the main west channel of the Tongzhou Shoal, alleviating the channel’s silting and shrinking. However, the west channel was unable to maintain its water depth after dredging and will adjust and approach to equilibrium, whereas the local river regime of the east channel tended to be unfavorable. The mainstream of upstream segment of the Longzhuayan node moved rightward and the shoals and channels intertwined. The right side of the Tongzhou shoal was scoured, with a trend of further scour along the connecting channels on the Tongzhou shoal. The marginal shoal near the Yingchuan port in the segment downstream the Longzhuayan node was scoured to the left, and the submerged shoals -10 m under the tail of Xinkai shoal was scoured, which is unfavorable to navigation. Measures should be taken to protect the right side of the east channel in time, to renovate the Xinkai shoal, and to consider reclamation of the Tongzhou shoal. Such measures are conducive to maintain the long-term stability of the shoals and the flow diversion pattern of the bifurcation channel.