In order to resolve the contradiction between urban development and ecological low-carbon, carbon footprint is introduced into water resource allocation. We include water shortage rate and net carbon emission during water supply and water use processes in the overall objective function. Six constraints of water supply, carbon emission, water extraction, ecological water demand, minimum water supply guarantee rate and non-negative constraints are set to construct optimal regional water resources allocation model based on carbon footprint. The model is solved by the multi-objective programming method based on ideal point and genetic algorithm. Taking Feng County of Xuzhou as an example, the analysis and calculation of water supply and demand balance are carried out. The results show that Feng County is expected to reduce the water shortage rate by 6.2% and carbon emission by 5.8% in 2030.