The development of antibiotic-independent antimicrobial materials is of great significance due to the great challenge of drug resistance in antibiotic therapy. Novel graphene oxide-based nanocomposites with broad-spectrum antimicrobial activity against Gram-negative/positive bacteria, including drug-resistant bacteria, were prepared. Superhydrophilic polyethyleneimine (PEI) was attached on the surface of graphene oxide via covalent bonding, and then quaternized with bromoalkyl phosphonate to form functionalized ionic liquid (PFIL) layer. Futher hydrolyzation of phosphonates and loading metal ions afforded nanocomposites GO@PEI-PFIL-Mn+. GO@PEI-PFIL-Ag+ exhibited potent antimicrobial activity against E. coli and MRSA (MICs: 0.98 μg/mL, 7.81 μg/mL), and showed fast killing effects on E. coli, S. aureus, and MRSA (~99%, ~99% and ~98% reduction in 2.5 h, respectively). The excellent potency can be attributed to the sharp shear effect of graphene oxide, the interaction between the positively charged material and the negatively charged bacterial cell membrane, and the combination of silver ions with the sulfhydryl (-SH) and other groups in the body of the bacteria, which generates reactive oxygen radicals (ROS). These novel nanocomposites show great potential in the treatment against drug-resistant pathogenic bacteria.