The basin cleaner production was discussed based on the theory and methodology of industrial ecology, circular economy, sustainable development and systemic theory. Using the basic theory of cleaner production, combining the requisition of cleaner production from practice in China, the implementation level of cleaner production was improved from company to basin. The theoretical basis and methodology for basin cleaner production was also discussed. And the system dynamics model of basin cleaner production potential (SDM-BCPP) was established. The emission-reduction contribution of basin cleaner production was analyzed in the case of Liaohe River basin. The technology roadmap among basin cleaner production was presented from the case study.