As a traditional means of transportation, water transportation has many advantages, such as larger capacity, lesser energy consumption, lower cost and lesser land occupied. In recent years, water transportation in China has been rapidly developing. Among them, waterway regulation engineering plays a very important role in smoothing waterway; ensure waterway security and promoting sustainable economic development. Meanwhile, waterway regulation projects have threatened the ecosystem of rivers. In this paper, the three dimensional hydrodynamic and sediment transport model combined with fish habitat model are built to simulate the environmental and ecological responses for the waterway regulation engineering. The model was used to perdition the fish habit change by waterway regulation which for improving navigable depth at the Jieshou reach of Xijiang River, China. The numerical results show that, waterway regulation increases the diversity of hydrodynamic environment and habitats. The better fish habitat area is increase during drought and flood period, and decrease slightly during middle-flow period.