Due to Yangtze Estuary Deepwater Channel Regulation Project with 40 years of research and 13 years of construction, the 12.5-meter-deep waterway was officially navigational in May 2011, and thus the pattern of Yangtze estuary waterway system had a historic change and stepped into the period of post 12.5-meter navigation channel. Based on analysis of current situation and problems of Yangtze estuary waterway, various kinds of opportunities and challenges of Yangtze estuary waterway in the period of post 12.5-meter navigation channel are discussed, and relevant channel regulation measures are preliminarily presented.