The 12.5-meter-deep waterway of the Yangtze estuary has stepped into a new stage of stable operation and obvious benefit, but the navigational resources of the North Channel and South Passage in the Yangtze River estuary are abundant, which still have the potential of further development. Combining with the new situation and requirements of the Yangtze estuary waterway development, we point out that the future development keypoint of the Yangtze estuary waterway is the North Channel. By summing up practical experience of the Yangtze River Estuary Deepwater Channel Regulation Project, we probe into the general principles of the Yangtze estuary waterway regulation under the new situation. According to the differences of stream pattern feature, fluvial evolution characteristics and navigation-obstructing properties along the waterway of the North Channel, we propose relevant channel regulation ideas and principles of the upper, middle and lower reaches of the North Channel are respectively.