In china river shipping not only contribute to the development of the economy, but also damage the environment waters. It is very important to design effective mechanism and policy for controlling water pollution. This paper designs a effective mechanism to control river shipping water pollution through process controlling as angle of view based on the analysis of the reason and characteristic of water induced by river shipping pollution. In order to validate the effect of the mechanism this article also simulate the controlling mechanism and policy based on system dynamics model by using tree-structure methodology. The results are helpful to the sustainable development planning between river shipping and water environment.