In this study, an inclusion complex of apigenin (AP)-hydroxypropyl-β-cyclodextrin (HP-β-CD) was prepared via supercritical antisolvent (SAS) method using N, N-dimethylformamide (DMF) as solvent and carbon dioxide as antisolvent. The mole ratio of AP and HP-β-CD (1:1) was established by phase solubility equilibrium experiment. The optimal conditions were determined through single-factor experiments; these conditions included precipitation pressure of 22.5 MPa, precipitation temperature of 50 °C, and AP concentration of 20 mg/ml. The load efficiency and encapsulation efficiency of the AP-HP-β-CD inclusion complex, with a mean particle size of 392.13 ± 7.56 nm, were 13.97% ± 0.17% and 93.22% ± 1.17%, respectively, under the optimal conditions. FTIR, 1H NMR, SEM, XRD, DSC, and TG analyses were also conducted. Results showed that the inclusion complex was formed because of the interaction between AP and HP-β-CD. DMF residue in the inclusion complex was 0.033% lower than the ICH limit for class II solvents. The solubility of the inclusion complex was approximately 152.43 times higher than that of the raw AP. In the in vitro study, the dissolution rate of the AP-HP-β-CD inclusion complex was about 7.60 times higher than that of the raw AP. In the in vivo study, the bioavailability of the inclusion complex increased by 6.45 times compared with that of the raw AP. Hence, the prepared AP-HP-β-CD inclusion complex exhibits potential as a new oral therapeutic agent formulation for clinical applications.