Metal-organic frameworks (MOFs) are attracting considerable attention as a result of their unique structural properties, such as a high surface area, highly porous topology, and tunable size and shape, which enable them to have potential applications as a new class of carriers for functional agent or drug delivery. However, most of the MOFs and the polymers used are not pharmaceutically acceptable. For the first time, this study successfully conducted the rapid synthesis of cyclodextrin metal-organic frameworks (CD-MOFs) through a facile and green seed-mediated method. The size control, crystal structure, and thermal properties of CD-MOFs with and without seeds were investigated. When 1 mg/mL seed was added, the size of γ-CD-MOF crystals decreased from 6.2 ± 0.8 to 1.8 ± 0.4 μm. The CD-MOFs synthesized though the seed-mediated method had higher crystallinity and thermal stability than those that were not. Furthermore, the CD-MOFs could encapsulate hydrophobic molecules, such as Nile red (NR), which was chosen as a model, and the interaction mechanism between γ-CD-MOFs and NR was investigated. Results showed the formation of a 1:1 complex between NR and CD-MOFs, demonstrating the potential of these polymers as carriers for hydrophobic drug delivery applications.