On the basis of comprehensive investigations of reasons to result in different efficiency not only in civil but also in abroad countries, combined with specific situation of navigation and hydropower projects of Guizhou Province, the mechanism corresponding to the organization is established roughly via the following measures: to follow the thinking and requirements of CMM and ISO system and to apply them to daily management; the factors to cause problem of blocked water transport of the navigation and hydropower projects to be explored, the reasons were studied to find out the methods which can finally overcome these difficulties; to analysis the measures which can improve the management efficiency and to study the reasons which hind behind them. On the conditions to start the whole equipment and scientific method possessed by the navigation and hydropower projects of Guizhou Province, the scheme of mechanism system suitable to navigation and hydropower projects of Guizhou Province is roughly developed, which has the quantitative, traceable, and continuous improvement properties. The studied results may be valuable to other similar mountain river cases in other places.