From the concept of regional sustainable development, this paper established the coordinate assessment index system of regional industrial structure and water utilization structure on the condition of reasonable utilization of water resources and not sacrificing the water environment. Using the sort of set pair connection degree analysis of identical discrepancy contrary state, this study proposed a coordinate development index formula of regional industrial structure and water utilization structure by the reference to the growth curve formula and built the coordinate assessment model of regional industrial structure and water utilization structure based on set pair analysis. Applying the model to Shandong Province, the results are in accordance with the fact, the calculation process is concise, and the model has high operability. Research results can provide scientific and effective decision-making basis for regional water resources development.