Water resources are the foundation that mankind depends on for his existence and development. In order to realize the sustainable development of the society and economy, we must give more consideration to the comprehensive evaluation about regional water utilization level. The method of Set Pair Analysis (SPA) is used to study the relationship between certainty and uncertainty among the objective things and its core is to compute the connection degree among the things. The paper puts forward a new method based on SPA to build the evaluation standards according to the actual conditions of regional water utilization. Employing this new method, the paper studies the water utilization level of the area along the lower Yellow River quantitatively, and compares the evaluated results with the results from multi-hierarchy grey relation comprehensive evaluation model (MGRCEM). The comparison shows that the overall results from the SPA method are consistent with those from MGRCEM. Moreover, the SPA method has many advantages such as convenient and simple computation, objective and reasonable evaluation results and so on. The applied method can serve as a new approach for water utilization studies, and the evaluation standards built in the paper can solve some evaluation problems of regional water utilization level effectively.