Organization and management of water conservancy projects is an important content and guarantee of water resources,and changed with external environment. Higher requirements is required due to three red line in water resource management, modern theory in project management, sustainable development theory in water conservancy, it is necessary to reform and innovation for organization and management system of water conservancy projects. Present water conservancy engineering management system is analyzed, and innovation countermeasures are discussed combining with the current problems in project organization and management system.