In recent years, nanomaterials have been widely used in the biomedical field. The biphenylene network is a highly promising planar carbon nanomaterial. To better explore its biomedical applications, we need to understand the biological effects of the biphenylene network. To investigate the biological effects of the novel nanomaterial biphenylene network, we used molecular dynamics simulations to study the interactions of the novel planar carbon nanomaterial biphenylene network with α-helical and β-sheet proteins. We found that both types of proteins adsorb flatly on the surface of the biphenylene network; the strong van der Waals interaction is the main adsorption force, while π-π stacking also provides an auxiliary force for the adsorption. When the HP35 protein whose secondary structure is an α-helix was adsorbed on biphenylene network, the entire structure of α-helix 2 was disrupted and α-helix 3 partly recovered its helical structure after being disrupted. In contrast to the β-sheet YAP65 protein, only part of the structure of β-sheet 1 was disrupted. Therefore, the biocompatibility of the biphenylene network with the β-sheet YAP65 protein is better than that of the α-helical HP35 protein, which may be due to the different surface curvature of the protein's secondary structure. Our research promotes the application of the biphenylene network in biomedicine and provides a theoretical basis and experimental direction for practical experiments.