Photodynamic inactivation that can directly utilize renewable solar energy for sterilization has attracted widespread attention in countering global environment deterioration and bacterial pollution. Graphitic carbon nitride (g-C3N4), a metal-free polymeric semiconductor with a mild band gap (2.7 eV), excellent optical properties and physicochemical stability, has become a hot-spot in photocatalytic sterilization. Nanostructured materials have shown great potential in improving the photodynamic inactivation efficacy of bulk g-C3N4. This review systematically analysed and summarized the latest studies on g-C3N4 based nanostructured materials for photodynamic inactivation. First, strategies to enhance the sterilization of g-C3N4-based nanostructured photodynamic inactivation materials and their contemporary challenges are briefly introduced. Second, the light source and synthetic methods are described. Third, the targeted inactivation organisms, including Gram-negative bacteria, Gram-positive bacteria, drug-resistant bacteria, harmful algae and bacteriophage, are described. In addition, the photocatalyst concentration, corresponding efficacy and mechanisms of sterilization are discussed. Finally, the deficiency and possible future perspectives of g-C3N4-based nanostructured photodynamic inactivation materials are articulated.