Conventional antibiotic therapies are becoming less efficient due to the emergence of antibiotic-resistant bacterial strains. Development of novel antibacterial material to effectively inhibit or kill bacteria is crucial. A graphene-based photothermal agent, magnetic reduced graphene oxide functionalized with glutaraldehyde (MRGOGA), was synthesized for efficient capture and effective killing of both gram-positive Staphylococcus aureus (S. aureus) and gram-negative Escherichia coli (E. coli) bacteria upon near-infrared (NIR) laser irradiation. In the present work, we took advantage of the excellent photothermal properties of reduced graphene oxide upon NIR laser irradiation and glutaraldehyde as an efficient capturing agent toward both bacteria. Its magnetic characteristic allows bacteria to be readily trapped in a small volume by the external magnet. The synergetic effects increase the heating extent by MRGOGA upon NIR laser irradiation and the killing of the captured bacteria. The survival rate and membrane integrity assay demonstrate that 80 ppm MRGOGA solution provided rapid and effective killing of up to 99% of both gram-positive and gram-negative bacteria in 10 min upon NIR laser irradiation under batch operation mode. Graphene demonstrated better photothermal antibacterial efficiency than carbon nanotubes. Furthermore, a microfluidic chip system under continuous operation mode demonstrates the reusability of MRGOGA and offers a biocompatible platform for online phothothermal sterilization.