It is well known that the limited aqueous solubility of some drugs often reduces their bioavailability to targets. Inclusion complex formation of drugs with β-cyclodextrin is one of the best approaches for drug delivery improvement. Extensive microscopic molecular dynamics simulations were performed to study the interactions between β-cyclodextrin and a class of kinase inhibitor drugs. Solvation free energy calculations demonstrated that these drugs are insoluble in water and reinforced the need for a carrier to increase the solubility. The binding of these drugs into β-cyclodextrin was assessed by calculating the binding free energy, and it was found that all drugs tended to be bound thermodynamically. Examination of the dynamic properties showed that the drugs were loaded into β-cyclodextrin, so due to the loading of drugs into the β-cyclodextrin, the mean square displacement (MSD) of all the drugs drastically decreased. The loading of drugs was accompanied by pushing of water out of the center of the β-cyclodextrin cavity. The drugs showed different orientations and mechanisms for loading into β-cyclodextrin. By studying the root mean square fluctuation (RMSF), it was revealed that the drugs were flexible in interaction with β-cyclodextrin; in contrast, β-cyclodextrin retained its rigidity in all simulated systems.