Background The kinase of Aurora A has been regarded as a promising therapeutic target due to its altered expression in various human cancers. However, given the high similarity of the active binding site of Aurora A to other kinases, designing highly selective inhibitors towards Aurora A remains a challenge. Recently, two potential small-molecule inhibitors named AT9283 and Danusertib were reported to exhibit significant selectivity to Aurora A, but not to Gleevec. It was argued that protein dynamics is crucial for drug selectivity to Aurora A. However, little computational research has been conducted to shed light on the underlying mechanisms. Methods In this study, MM/GBSA calculations based on conventional molecular dynamics (cMD) simulations and enhanced sampling simulations including Gaussian accelerated MD (GaMD) simulations and umbrella sampling were carried out to illustrate the selectivity of inhibitors to Aurora A. Results The calculation results from cMD simulation showed that the binding specificity is primarily controlled by conformational change of the kinase hinge. The protein dynamics and energetic differences were further supported by the GaMD simulations. Umbrella sampling further proved that AT9283 and Danusertib have similar potential of mean force (PMF) profiles toward Aurora A in terms of PMF depth. Compared with AT9283 and Danusertib, Gleevec has much lower PMF depth, indicating that Gleevec is more easily dissociated from Aurora A than AT9283 and Danusertib. These results not only show the selective determinants of Aurora A, but also provide valuable clues for the further development of novel potent Aurora A selective inhibitors.