The original ecological footprint model of water resources was improved here to explore the rational policy of water resources development and utilization. Aiming to address the problems of high complexity, weak applicability, and insufficient systematicness and dynamics of the existing water resources ecological footprint model, the grey water footprint was introduced into the model to quantify the water for decontamination. In the calculation of the water resources ecological footprint index, the rainwater collection project, seawater desalination, and water resources regeneration, unconventional water sources were considered, and when combined with the system dynamics simulation technology, the SD model of water resources sustainable utilization in China was established. We carried out research on the regulation and control of sustainable utilization of water resources in China. The results showed that the development and utilization of water resources in China remained within the ecological carrying capacity as a whole from 2000 to 2017, and the development of water resources still had potential, but the supply and demand of water resources were unbalanced. Given this, from the perspective of throttling, open-source, and pollution control, six control schemes for sustainable utilization of water resources in China were set up, including the continuation of the current situation, green throttling, pollution control, strict planning for water source development, and comprehensive treatment. Among them, the comprehensive coordination plan for 2018-2050 could properly solve the problem of water resources supply and demand under the conditions of meeting the ecological sustainability of water resources and reasonable water resources load and was the best regulation plan to realize the sustainable utilization of water resources in China. At present, the development of water resources in China lags, which does not match the growth rate of social and economic development on water resources consumption. It is necessary to further strengthen the efforts of open-source, water-saving, and pollution control based on the original policies, so as to alleviate the ecological stress of water resources.