The drug-resistant bacteria, particularly multidrug-resistant bacteria, has emerged as a major global public health concern posing serious threats to human life and survival. Nanomaterials, including graphene, have shown promise as effective antibacterial agents owing to their unique antibacterial mechanism compared with traditional drugs. Despite the structural similarity to graphene, the potential antibacterial activity of carbon nitride polyaniline (C3N) remains unexplored. In this study, we employed molecular dynamics simulations to investigate the effects of the interaction between the C3N nanomaterial and the bacterial membrane to evaluate the potential antibacterial activity of C3N. Our results suggest that C3N is capable of inserting deep into the bacterial membrane interior, regardless of the presence or absence of positional restraints in the C3N. The insertion process also resulted in local lipid extraction by the C3N sheet. Additional structural analyses revealed that C3N induced significant changes in membrane parameters, including mean square displacement, deuterium order parameters, membrane thickness, and area per lipid. Docking simulations, where all the C3N are restraint to a specific positions, confirmed that C3N can extract lipids from the membrane, indicating the strong interaction between the C3N material and the membrane. Free-energy calculations further revealed that the insertion of the C3N sheet is energetically favorable and that C3N exhibits membrane insertion capacity comparable to that observed for graphene, suggesting their potential for similar antibacterial activity. This study provides the first evidence of the potential antibacterial properties of C3N nanomaterials via bacterial membrane damage and underscores the potential for its use as antibacterial agents in the future applications.