The construction of Gezhouba dam has blocked the migration path of the Chinese sturgeon and forced the formation of a new spawning ground for Chinese sturgeon natural reproduction in the downstream of Gezhouba. The operation of the Three Gorges dam changed the natural course of the river flow and the hydrodynamic characteristics of the Yangtze river. This is bound to affect the aquatic environment of Chinese sturgeon. Based on the many years of monitoring data and numerical simulation results for the Chinese sturgeon spawning ground, this article analyzed the effects of the Three Gorges and Gezhouba projects' operation to the Chinese sturgeon natural reproduction, and proposed measures to relieve the adverse effects. The results can provide the reference to protect the sturgeon resources and to maintain the balance of the Yangtze River ecosystem.