Recent experiments have found that fullerenols can inhibit coagulation factor X (FXa) activity and have the effects on anticoagulation. But the interactions between fullerene derivatives and FXa are still lacking which are crucial for the new inhibitors designs and applications. In this study, we investigated the interaction principle between FXa and fullerenol molecules (C60(OH)24)/carboxyfullerene molecules (C60(C(COOH)₂)₂) with different hydrophilic-hydrophobic properties via AutoDock Vina. We performed molecular docking to obtain the binding mode conformations of C60(OH)24/C60(C(COOH)₂)₂ to FXa and investigated multibody adsorption behaviors of C60(OH)24/C60(C(COOH)₂)₂ to FXa. Then we analyzed the interactions between FXa and C60(OH)24/C60(C(COOH)₂)₂ to obtain the absorption driving mechanism. We found C60(C(COOH)₂)₂ was more stable to bind to the active site of FXa compared with C60(OH)24 with lower binding energy during the competitive absorptions. The adsorption behaviors of fullerene derivatives C60(OH)24 and C60(C(COOH)₂)₂ were different as well during their multibody absorptions. The absorption of C60(OH)24 was driven by hydrophilic interactions while that of C60(C(COOH)₂)₂ was driven by hydrophobic interactions. These results can be used to guide the design and optimization of the fullerene derivative anticoagulant through inhibiting the activity of FXa.