Oxygenated polycyclic aromatic hydrocarbons (OPAHs) are toxic and carcinogenic compounds widely present in the natural environment, posing a serious threat to the environment and human health. However, the removal of OPAHs is mainly hindered by their low water solubility. Cyclodextrins (CDs) are frequently used to form inclusion complexes (ICs) with hydrophobic molecules to improve their solubility. In this study, we investigated the solubility enhancement ability of different CDs on 9-fluorenone, a common OPAH, through phase solubility experiments. We successfully prepared three solid ICs of 9-fluorenone with β-, hydroxypropyl-β-(HP-β-) and sulfobutylether-β-CD (SBE-β-CD) using the cooling crystallization method for the first time and characterized them via powder X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, etc. Molecular dynamics simulations were employed to investigate the binding modes and stable configurations of the ICs in the liquid phase and to explore the factors affecting their solubility enhancement ability. The results showed that all the CDs had a solubility enhancement effect on 9-fluorenone, with SBE-β-CD displaying the strongest effect, increasing the solubility of 9-fluorenone by 146 times. HP-β-CD, β-CD, α-CD, and γ-CD followed in decreasing order. Moreover, 9-fluorenone formed a ratio of 1:1 ICs to CDs. In addition, the interaction energy between SBE-β-CD and 9-fluorenone was the lowest among the CDs, which further validated the results of the phase solubility experiments from a theoretical perspective. Overall, this study provides a green method for the removal of 9-fluorenone pollutants in the environment and is expected to be applied to the removal and environmental remediation of other OPAHs.