Oral drug administration has become the most common and preferred mode of disease treatment due to its good medication adherence and convenience. For orally administered drugs, the safety, efficacy, and targeting ability requirements have grown as disease treatment research advances. It is difficult to obtain prominent efficacy of traditional drugs simply via oral administration. Numerous studies have demonstrated that cyclodextrins (CDs) can improve the clinical applications of certain orally administered drugs by enhancing their water solubility and masking undesirable odors. Additionally, deeper studies have discovered that CDs can influence disease treatment by altering the drug pharmacokinetics (PK) or pharmacodynamics (PD). This review highlights recent research progress on the PK and PD effects of CD-based oral drug delivery in disease therapy. Firstly, the review describes the characteristics of current drug delivery modes in oral administration. Besides, we minutely summarized the different CD-containing drugs, focusing on the impact of CD-based alterations in PK or PD of orally administered drugs in treating diseases. Finally, we deeply discussed current challenges and future opportunities with regard to PK and PD of CD-based oral drug delivery formulations.