How to transfix and realize orient run-through on Three Gorges Reservoir sector, Yangtze has been being a focus and disputation problem of academic circle historically. By the author research, the transfixion of Three Gorges Reservoir sector was not a simple one between the water systems of Jianghan plain and Sichuan basin, but a complex interweaving one among the two and many other middle to mini basins around Three Gorges Reservoir sector. The transfixion was achieved not only by retrogressive erosion of surface water, but also by dissolution, weathering and erosion of groundwater. The route of surface water might be different from the one of groundwater, and the underground river was given out by groundwater, whereas the sharp gorge was generated through the top collapse of underground river. The main watercourse of Yangtze was made of some surface river sectors and underground rivers. Though there existed orient and westward discharges, but there was no fixed watershed, and the current orientations among some sub sectors varied frequently cause of variation of rainfall in different basins. Since the down cut of the river and the earth's surface was eastward declined by neotectonic movement, the river to Sichuan basin was eastward deviated and the Yangtze made up. Three Gorges is a young river sector, it is not very long to become entirely surface river and realize orient run-through. Those recognitions will make significance to deepen genetic theory on large river.