The abuse of conventional antibiotics leads to increasing bacterial resistance. Nanozyme is a new kind of ultra-efficient and safe nanomaterial with intrinsic enzyme-like activities, showing remarkable potential as a next generation nanobactericide. Graphdiyne (GDY) is a burgeoning two-dimensional (2D) carbon allotrope with intriguing physicochemical properties, holding a great promise as a metal-free nanozyme. In this study, a boron doped GDY nanosheet (B-GDY) was constructed to simulate the performance of peroxidase (POD). By promoting the decomposition of H₂O₂ to produce reactive oxygen species (ROS), the bactericidal efficacies against both Gram-positive and Gram-negative bacteria were substantially enhanced attributed to the extremely high catalytic activity of B-GDY. In-depth density functional theory (DFT) calculations illuminate that doping of boron can introduce more active B-defect sites as well as lower Gibbs free energy during the H₂O₂ decomposition reaction. Notably, B-GDY contributes to significant wound healing and excellent biocompatibility, reducing the biological burden. The design of this nanozyme opens a new avenue for the development of alternative antibiotics.