In the design, construction and operation periods of the Three Gorges Project (TGP), great challenges have been met in different fields such as water resources and hydropower project construction, electromechanical equipment manufacture and ecological environment protection. In view of the key techniques and difficulties in the construction period, S&T breakthrough have been performed by the experts and scholars of various fields and a series of innovative achievements are gained, which make the scientific and technological levels in relevant fields improved. Some major innovative achievements gained in the TGP construction and operation are enumerated, which are significant for the hydropower project construction and clean energy development in the future in China.