The design of a bioactive surface with appropriate wettability for effective protein immobilization has attracted much attention. Previous experiments showed that the adsorption of hydrophobic protein HFBI onto a polydimethylsiloxane (PDMS) substrate surface can reverse the inherent hydrophobicity of the surface, hence making it suitable for immobilization of a secondary protein. In this study, atomistic molecular dynamics simulations have been conducted to elucidate the adsorption mechanism of HFBI on the PDMS substrate in an aqueous environment. Nine independent simulations starting from three representative initial orientations of HFBI toward the solid surface were performed, resulting in different adsorption modes. The main secondary structures of the protein in each mode are found to be preserved in the entire course of adsorption due to the four disulfide bonds. The relative binding free energies of the different adsorption modes were calculated, showing that the mode, in which the binding residues of HFBI fully come from its hydrophobic patch, is most energetically favored. In this favorable binding mode, the hydrophilic region of HFBI is fully exposed to water, leading to a high hydrophilicity of the modified PDMS surface, consistent with experiments. Furthermore, a set of residues consisting of Leu12, Leu24, Leu26, Ile27, Ala66, and Leu68 were found to play an important role in the adsorption of HFBI on different hydrophobic substrates, irrespective of the structural features of the substrates.