Infectious diseases caused by pathogenic bacteria and viruses pose a great threat to the ecological environment and the lives and health of humans and animals. Developing efficient bacterial inactivation techniques and nanomaterials prevent the invasion of pathogenic bacteria has become the goal pursued by researchers. Carbon materials exhibit enormous potential for bacterial inactivation applications due to their excellent biocompatibility, environmental friendliness, and high antibacterial performance. Graphdiyne (GDY), as a novel two-dimensional carbon material, has attracted widespread attention in the fields of biology and antibacterial due to its unique acetylene bonds, easily tunable electronic structure, good biocompatibility and peroxidase-like properties etc. This review summarizes the research progress of GDY and GDY-based nanomaterials, including pristine GDY, graphdiyne oxide (GDYO), heteroatom doped-GDY, and GDY-based composite materials in the field of bacterial inactivation, and discusses the opportunities and challenges faced by GDY-based nanomaterials in the fields of biomedicine and antibacterial in the future.