The Cyclodextrin (CD) encapsulation technology can significantly enhance the water solubility of Curcumin (CUR) and effectively protect it against chemical degradations. In the current study, a combination of experimental and multi-scale computational approaches was used to investigate the binding mechanism between CUR and β-CDs (β-CD, 2-HP-β-CD, Me-β-CD, and DM-β-CD). Phase solubility studies showed that β-CDs exhibited a strong binding affinity with CUR and significantly enhanced its solubility. SEM, PXRD, DSC, and TG analysis confirmed the formation of inclusion complexes, resulting in the transition of CUR from crystalline to an amorphous state. FTIR, 1H, and 13CNMR spectra deduced that CUR may have multiple binding conformations with β-CDs. The rationality of molecular dynamics simulation systems was confirmed by comparing the simulated IR spectrum from quantum mechanics with the experimental IR spectrum. MM-PBSA and umbrella sampling simulation calculated the binding free energy of the CUR/CD inclusion complexes, ranking Me-β-CD > DM-β-CD > 2-HP-β-CD > β-CD, and clarified that van der Waals interaction played a major role in stabilizing the inclusion complexes. RDF analysis confirmed that the release of high-energy water molecules drove the formation of the CUR/CD inclusion complex, and the β-CD substituents affected their exterior hydration layer. Additionally, principal component analysis (PCA) and non-covalent interaction analysis revealed three CUR/CD binding modes: bead-on-string, terminal insertion, and V-shaped-folding. The research strategy adopted here can serve as a paradigm for investigating the encapsulation mechanism of poorly soluble drugs with CDs.