Constructing a reasonable evaluation index system is important for characterizing water and land resources and for ecological restoration. To solve random and incomplete problems using a traditional evaluation index system, a novel model for evaluating regional agricultural water resources using a resilience index system was proposed. In addition, a new method for an evaluation index system and the filtering of key indicators were investigated. Based on the structural characteristics of a regional agricultural water resource system (AWRS), the model for an evaluation index system was built by constructing a hierarchical indicator architecture using a hierarchical framework model. The index weight was calculated using criteria importance through intercriteria correlation (CRITIC). Then, index completeness was ensured using principal component analysis, and the reliability of the results was tested using the analytic hierarchy process. The model was applied to the Jiansanjiang Administration of Agricultural Reclamation in Heilongjiang, China. The main results included the following: (1) the index was optimized from 46 to 32, which identified the key indicators that affect the resilience of the Jiansanjiang Administration AWRS, and (2) an evaluation index system was constructed with a completeness of 85.6%. The results of this study provide an important and practical model for studying the resilience of related resources and environmental fields.