Nanomaterials (NMs) have been widely used in the biomedical field. To explore the biological effects of graphene as one of the most widely used NMs, we studied the adsorption behavior and induced conformational changes of proteins representing different secondary structures on graphene: β-strands (WW domain), mixed α/β structure (BBA protein), and α-helices (λ-repressor). Our results indicate these model proteins were adsorbed onto the graphene surface quickly and tightly, however, varied degrees of conformational changes were observed. During the adsorption process, we found the β motif is a stiffer structural unit than the α-helix. Moreover, the level of conformational changes of the proteins is related not only to their sequence and structural properties but also to their orientation. Overall, from the different levels of intermolecular interaction, the protein adsorption was driven by van der Waals, hydrophobic and π-π stacking interactions. Our work suggests that classical molecular dynamics simulations and MM-GBSA calculations can provide useful information about the dynamics and energetics of the adsorption of proteins onto graphene. We believe that these findings will help us to further understand the adsorption of proteins on hydrophobic carbon nanomaterials at the atomic level.