Abstract:This paper systematically introduced the current situation of the implementation of the major science and technology program for water pollution control and treatment (The following is referred to as "water special project"). The problems existing in the implementation of administrative organization of water special project were analyzed from the aspects of project management mechanism, supervision mechanism, assessment and incentive mechanism. The problems existing in the implementation of technical management organization of water special project were analyzed from aspects of technical organization, technological breakthrough, and transformation of technological achievements. Optimization suggestions were put forward for implementing the management system of water special organizations. From the level of administrative management, (1) clearing the positioning of the special water function, clarifying the task boundary, and forming a broad consensus; (2) establishing a coordination mechanism to ensure the smooth connection between the relevant parties in the implementation of the water special project organization; (3) innovating research and development model, establishing specialized institutions, and promoting the deep integration of administration and technology. From the level of technology management, (1) unifying index system and implementing Performance evaluation mechanism which is suitable for the management characteristics of water special project; (2) strengthening the output of landmark achievements, breakthroughing major and key technologies, and forming a complete set of technology and equipment. (3) building the platform for the transformation of results, promoting the industrialization of Technology, and solving the problem of "two skins" in scientific research management and achievement transformation.