Grape seed extract (GSE) displays strong antioxidant activity, but its instability creates barriers to its applications. Herein, three HP-β-CD/GSE inclusion complexes with host–guest ratios of 1:0.5, 1:1, and 1:2 were successfully prepared by co-precipitation method to improve stability. Successful embedding of GSE in the HP-β-CD cavity was confirmed by fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM) analyses. The Autodock Tools 1.5.6 was used to simulate the three-dimensional supramolecular structure of the inclusion complex of 2-hydroxypropyl-β-cyclodextrin and grape seed extract (HP-β-CD/GSE) by molecular docking. The MALDI-TOF-MS technology and chemical database Pubchem, and structural database PDB were combined to reconstitute the three-dimensional structure of target protein. The binding mode of the HP-β-CD/GSE inclusion complex to target protein was studied at the molecular level, and the antioxidant ability of the resulting HP-β-CD/GSE inclusion complexes was investigated by measuring 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging. The effects of HP-β-CD/GSE on myofibrillar protein from lamb tripe were also investigated under oxidative conditions. The positions and interactions of the binding sites of HP-β-CD/GSE inclusion complexes and target protein receptors were simulated by molecular docking. The results showed that HP-β-CD/GSE inclusion complexes were successfully prepared, optimally at a molar ratio of 1:2. At low (5 μmol/g) to medium (105 μmol/g) concentrations, HP-β-CD/GSE inclusion complexes decreased the carbonyl content, hydrophobicity, and protein aggregation of myofibrillar protein from lamb tripe, and increased the sulphydryl content. Furthermore, high concentration (155 μmol/g) of HP-β-CD/GSE inclusion complexes promoted protein oxidation.