Cyclodextrin-based nanosponges are widely investigated for several applications and are considered potential drug carriers. The method of nanosponges preparation involves the use of chemical cross-linking agents where the properties of Nanosponges can be affected. This study compared the resulting differences in the final nanosponges' properties using carbonate and dianhydride crosslinkers. Diphenyl carbonate and EDTA dianhydride were used for the synthesis of nanosponges. Both types of nanosponges were loaded with curcumin as a model drug. Physicochemical characterizations, including PXRD, DSC, FTIR, scanning electron microscopy, AFM, particle size, zeta potential, and surface area analysis, were carried out for the prepared nanosponges. Curcumin release and drug content were also evaluated. Nanosponges prepared by Diphenyl carbonate crosslinker resulted in an amorphous form compared to crystalline EDTA-nanosponges. This study reported the successful inclusion and complexation of curcumin inside carbonate cross-linked cyclodextrin-based nanosponges and suggested the physical entrapment of crystalline curcumin in EDTA dianhydride. These findings were further investigated and supported by computational modeling.