In view of uncertainty and complexity in the process of urban water security assessment, Set Pair Analysis Model (SPAM) is adopted. Specially, in this study, the model is improved from two aspects: (1) three-element connection degree is expanded to multi-element connection degree, which makes the depiction of state space more accurate; (2) credible degree criterion and marking criterion are combined to analyze the assessment results. The improved model is applied to Wuhan city, China. The evaluation indicator system with clearly logic and hierarchy are built and the weight of each indicator is confirmed by the analytical hierarchy process (AHP). The evaluation results show that, overall, water security state of Wuhan is good and there is continuous improvement, which is in good agreement with the true situation. The comparison between the results of the model and two other evaluation methods verifies the rationality and reliability of the developed model. In addition, the results also indicate that the developed model is more accurate than ordinary SPAM. Consequently, it is concluded that the model can be an effective tool for urban water security assessment.