With social and economic development, carbon emissions mainly caused by fossil fuel consumption keep increasing. At the same time, the over exploration of water/land resources and occupancy of ecological water use have reduced the carbon-capture capacity of the ecosystem. These two situations result in the increase of regional net carbon emission. The rational allocation of water resources towards low-carbon development mode sets up the connection between carbon cycle and water resource system, which is based on the relationship between carbon emission and socio-economic water use and the relationship of carbon capture and water demand for ecosystem. It makes use of water saving measures to decrease the socio-economic water use and carbon emission. Furthermore, through the joint allocation of water resources and net carbon emission, it curbs the carbon emission and guarantees a better water supply for the ecosystem, which therefore strengthens the carbon capture capacity. Based on the generalization of regional carbon-water coupling system, it establishes the rational allocation model of water resources towards low-carbon mode and applies the model in the Baiyangdian Basin. The results indicate that water supply could not meet regional demand during 2005-2010 when the whole basin was carbon "source" due to increasing benefits of net carbon emission per cubic meter of water. If the economic-social development mode is extensional in the planning year of 2020, the high water-saving allocation scheme should be recommended, of which water deficit, amounts of carbon emission and net one will be reduced by 28.45%, 11.9% and 13.5% respectively. If it is low-carbon mode, medium water-saving scheme should be recommended and the above three targets will be reduced by 28.45%, 60.1% and 74.9%.