Based on the river dynamics theory, we derived a mathematical expression of waterway depth variation before and after erosion of the channel at regulation stage. Then, the theoretical analysis of the expression showed that waterway depth could increase. Under the erosion of the release of clear water from the Three Gorges Reservoir, in order to make the release of clear water only erode vertically, it is necessary to take several measures, that is, protecting key movable bottomlands, controlling dredged channel(not broadening in both sides), and protecting low bottomlands from erosion in dredged channel. Thus, protective control works play a positive role in improving waterway condition. Taking Ouchikou and Taipingkou segments of the Jingjiang River at the middle reach of the Yangtze River as examples, we computed the variation of waterway depth in both segments after protecting key movable bottomlands. The model derived results are in accordance with the variation of waterway depth resultant from generalized measured profile, which further verifies the effect of protective control works on improving the waterway condition.