A systematic investigation of intermolecular interactions of β- cyclodextrin(β-CD)and Nifedipine(Nif)in gas phase and in water were done by the mass spectrometry and DFT calculation method. The results obtained clearly indicated that the aromatic ring containing the nitro moiety of Nifedipine inverted into the wider rim of β cyclodextrin, the high collision induced dissociation (CID) energy in mass spectrometry experiments demonstrated the stability of the 1:1 Nif-β-CD complexes. Compared to the native β-CD, HP- β-CD and DM- β-CD are more easily to form complexes with Nif due to their approximately double lower binding energy, the thermodynamic parameters, HOMO, LUMO, the global reactivity descriptors of these complexes were calculated and interpreted. Furthermore, the study of natural bonding orbitals (NBO) and quantum theory of protons in molecules (QTAIM) supports the existence of various hydrogen bonds and van der Waals interactions in three complex structures, as predicted by chemical bonding principles. IGMH analysis give the visualized origin of weak attractive interactions between the CDs and the Nifedipine.