The evolution of the river regime in the north passage after the construction of the second phase of the Yangtze River deepwater navigation channel project from 2004 to 2007 is analyzed. The results show that the principle of “deposit in flood season while erosion in dry season” applies generally to the mouth bar zone of the north passage. Besides, the north beach of the upstream of the north passage deposits all the time. Deposition also happens on the south beach near W3, which leads to a high slope of the shoal. In addition, the nonlinear negative correlation effect between the depth ratio of the south shoal channel and the channel siltation volume is significantly strong. Several reasons can be concluded to explain the high siltation volume in the navigation channel, such as the continuous deposition at the W3 south beach, small depth ratio of the shoal channel, high slope of the beach and the fact that the width of the 8m-depth line is the smallest.