Dabigatran etexilate (DE) is a new oral anticoagulant drug used to prevent non valvular atrial fibrillation stroke and vascular embolism. DE itself has no pharmacological activity. Its active component is Dabigatran (DAB), the product of DE by catalyzed hydrolysis in plasma and liver. However, the interaction mechanism between the polar groups of DAB and thrombin is still unclear, especially in physiological conditions, although the drug has already been used for clinical treatment. No specific reversal agent has been found for dabigatran.This work used steady-state and time-resolved fluorescence spectroscopy methods to study the interaction between DAB and thrombin in pH 7.4 phosphate buffer. A combination of dynamic and static fluorescence quenching of thrombin when in contact with DAB wasobserved, suggesting that the electrostatic effect between thrombin and the benzamidine group of DAB was the key factor of a fast and effective formation of the DAB-thrombin complex. The molecular conformation of DAB when in interaction with thrombin was studied by molecular docking simulation and the effect of DAB polar groups on the binding energy was investigated. By comparing the fluorescence spectra and molecular docking simulation results of the interaction between thrombin and dabigatran ester (DE, esterification of both DAB polar groups), dabigatran ethyl ester (DAE, esterification of DAB carboxylic group), and dabigatran hexyl ester (DAH, esterification of DAB benzamidine group), the role of polar groups in the combination of dabigatran and thrombin was further verified. Steady-state and transient fluorescence spectra of DAB and DE interacting with bovine serum albumin (BSA) under physiological pH conditions were also obtained,confirming that the polar groups of DAB play an important role in the selective binding of DAB with thrombin. The results provide theoretical and experimental bases for improving the drug efficiency and finding reversal agents.