The renovation project of deepwater navigation channel at Yangtze estuary is located in the north channel and built in three phases. After construction of the project, the phenomenon of back silting is serious and the cost for dredging and maintaining is huge. With the establishment of 2D numerical model of deepwater navigation channel at Yangtze estuary,the paper calculated the flux of different sections in 1997, 2001, 2005, 2009, and analyzed the changes of flux during the construction of the project,and discussed the reason of back silting. The flow of ebb in the middle of the channel decreases while that in the upper increases after the construction of first phase. Besides, the flow of ebb decreases in the whole channel after the second phase project while the third phase project slows down the decreasing tendency. The decrease of ebb flow may be the hydrodynamic reason for back silting.