Abstract: National water resources monitoring capacity building project is an important measure to strengthen water resources and water quality monitoring capacity construction for water conservancy system. The co-building of laboratory for water environment monitoring in the Yangtze River Basin and the related area is an important way to realize monitoring and management of provincial boundary cross-section and important water function area. In this paper, the selection, construction, operation management, information management, potential problems and solutions of co-construction and co-management laboratory for water environment monitoring in Yangtze River Basin are introduced and analyzed. The analysis results indicate that developing the co-construction laboratory under current situation can achieve the multi-win for society, basin and local government, which is a useful attempt to mechanism innovation in implement the most stringent water management system.