Graphdiyne (GDY) as an emerging 2D carbon-network nanomaterial possesses many fascinating properties that lead to numerous exciting applications, but the use of GDY and its derivatives in the antibacterial field has not yet been discovered. In this study, we first report on the use and evaluation of GDY and graphdiyne oxide (GDYO) as antibacterial agents and propose the antibacterial mechanisms of GDY-based nanomaterials. GDYO has been synthesized via the surface oxidation of GDY, and the antibacterial activity of GDYO has been compared with that of GDY through a series of antibacterial tests. Surprisingly, surface oxidation endowed inert GDY with superior antibacterial capability against two representative bacterial models: Escherichia coli and Staphylococcus aureus. Antibacterial mechanism experiments disclose that the antibacterial function of GDYO is a result of reactive oxygen species-dependent oxidation stress when a dispersed GDYO suspension has a direct contact with bacteria especially under visible light irradiation.