This study intended to evaluate the effect of cyclodextrins on the apparent solubility and permeability of lipophilic drugs under physiological conditions and establish in silico model to choose the optimal amount of cyclodextrins for cyclodextrin-containing oral formulations. In order to study the effect of cyclodextrins under physiological conditions, bile salts and lecithin were added into the rat intestinal perfusion solution to simulate the fasted intestinal fluid. In addition, the in vivo oral absorption performances of cyclodextrin-containing formulations were simulated by gastrointestinal simulation technology based on the advanced compartmental absorption and transit model (ACAT). The permeability of progesterone was not significantly different between 0.1 mM and 1 mM of HP–β–CD under physiological conditions. When the concentration of HP–β–CD was 1 mM, the permeability of progesterone under physiological conditions was significantly higher than that in vitro. The in silicomodel established in this study was validated by in vivo studies of four formulations containing different dosage of cyclodextrin, proving that it was accurate and reliable. In conclusion, this work demonstrates the permeability of lipophilic drugs could not decrease quickly among a certain range of dosage of HP–β–CD in vivo. Studying the solubility-permeability interplay under physiological conditions would be more meaningful.