The tidal estuary is jointly influenced by the river flow and tidal current. The dynamic difference of the tidal current and river flow and their complex temporal and spatial variation result in obviously different characteristics of water and sediment in different river reaches. The characteristics should be taken into account during the study of estuary regulation. An intergraded method combining numerical model and physical model are consequently adopted in the estuary regulation. Due to the fact that numerical model and physical model have different features and application scopes, the research method and evaluation index should be reasonably selected according to the characteristics of water and sediment in a specific river reach and research purposes. Based on the practice of the Improvement Project of the Deep-draft Channel of the Yangtze Estuary, the application of comprehensive research of numerical model and physical model and their effects are presented.