This paper describes the hierarchical analysis performed on various cross-linking agents used for the preparation of cyclodextrin nanosponges, as a drug carrier for poorly soluble and unstable drugs. Prioritizing the right one is crucial for research considering the factors like time, cost materials, and simplicity of the process. A four-level hierarchy model was constructed for four different cross-linker types, namely, carbonyl, diisocyanate, anhydride, and epichlorohydrin based on different criteria and subcriteria involved in the preparation of cyclodextrin polymer. It applies the principle of pairwise comparison, priority vector generation, and synthesis. It restricts reprocessing due to inapplicable decisions. This methodology helped in prioritizing carbonyl cross-linkers with regard to simple and easy processing steps with minimum input materials and desirable physicochemical characteristics for nanosponges with the priority value of 32.4%. The cross-linker was prioritized with a minimum judgment error by consistency verification. This analysis helps minimize experiments, development process, and improved product quality of cross-linked cyclodextrin as a drug delivering carrier.