This study summarizes impacts of waterway transport business（include harbor,waterway construction,ships）on the water environment,atmospheric environment,environment and aquatic ecology,etc.in the Yangtze River.The result shows that the impacts are longterm,dispersive,stationary,mobile and complex.So we establish an integrated green waterway transport system(GWTS) which includes the main system(ecological harbor,ecological waterway and new-type ships) and auxiliary system(industry standards,environmental monitoring network and scientific research),which may serve as reference for the Yangtze River waterway transport construction and spreading of GWTS concept.