Nanobubbles have been proven existent at the liquid/solid interface, and become a focus of research on varied interfacial processes. In the present work, by observing in situ with atomic force microscope (AFM), we found that nanobubbles could influence the adsorption process of bovine serum albumin (BSA) on hydrophobic surface of highly ordered pyrolytic graphite (HOPG). BSA could adsorb evenly, and coexist with nanobubbles at water/HOPG interface. After removing nanobubbles by injecting ethanol, some hollows were found in the BSA layers at the same positions of nanobubbles existing previously. These hollows were about 8 nm in depth and dozens of nanometers in diameter. The correlation coefficient between the areas of nanobubbles and that of the corresponding hollows reached 0.88-0.94, which strongly supported the assumption that the hollows were indeed caused by the nanobubbles. Moreover, the BSA molecules formed rings around the nanobubbles, suggesting the preference of BSA adsorption onto the contact line at water/HOPG interface.