Graphene-based silver nanoparticles (Ag NPs-GE) material has been developed and demonstrated antibacterial effect against Escherichia coli and Pseudomonas aeruginosa. In this study, the antibacterial activity and mechanism on P. aeruginosa were investigated. The experiments results showed the minimum bactericidal concentration of Ag NPs-GE to P. aeruginosa is 20 μg/ml. When P. aeruginosa were exposed to 20 μg/ml Ag NPs-GE for 1 h, the cell wall was breakdown. In order to study the mechanism of antibacterial effect of Ag NPs-GE, two-dimensional electrophoresis was carried out to compare the protein expressional profiles of P. aeruginosa exposed to 5 μg/ml Ag NPs-GE or 5 μg/ml AgNO3 with the untreated bacteria. Identification of differentially expressed protein was performed by MALDI-TOF/TOF MS. The change of proteomic profile induced by Ag NPs-GE was distinct from that induced by AgNO3. Seven identified proteins were found induced and nine proteins were suppressed by Ag NPs-GE. Five identified proteins were found induced and twenty proteins were suppressed by AgNO3. In addition, either Ag NPs-GE or AgNO3 suppressed the expression of eight proteins, amidotransferase, 30S ribosomal protein S6, bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase, arginyl-tRNA synthetase, nitroreductase, acetolactate synthase 3, methionyl-tRNA synthetase and periplasmic tail-specific protease. Furthermore, gene ontology analysis and KEGG pathway analysis were used to characterize the functions of those proteins.