Using numerical simulation method, aiming at the Ouchikou reach and Guniusha reach in the middle reach of the Yangtze River which are typical navigation-obstructing shoals, the new method to determine waterway regulation parameters is applied to the specific section in waterway regulation construction after the Three Gorge Project reservoir using, practicing and testing the key parameters of waterway regulation, providing applied basis for relevant researches. The calculation results from the mathematical model show that under such regulation parameters, through typical hydrological processes the designed channel dimensions and the expected effect of regulation can be achieved. The results of the waterway regulation parameter theory results apply to the shoals regulation in the middle reach of the Yangtze River after utilization of the Three Gorges reservoir.