The development of branch channel will certainly destabilize the navigation condition in main channel. Hence the restrictive measures on developing branch channels are carried out in recent waterway regulation projects. This paper carries out a comparison study on flow and sediment transport characteristics based on the before and after project observed data in Majiazui channel. The flow dynamic conditions of branch channel development and the effect of the controlling projects are also analyzed from the standing point of the adaptation of river dynamic. Moreover, the deficiency of the Majiazui waterway regulation project and the improvement measures are also presented. The cognitions of branch channel waterway regulation are also summarized based on above analyses.