With the increased prevalence of antibiotic-resistant infections, there is an urgent need to develop novel antibacterial materials. In addition, gaining a complete understanding of the structural features that impart activity toward target microorganisms is essential to enable materials optimisation. Here we have reported a rational design to fabricate antibacterial supramolecular nanoparticles with variable shape, size and cationic group density, by exploiting noncovalent interactions between a shape determining template amphiphile and a cationic amphiphile to introduce charge on the nanoparticle surface. We have shown that the monomeric cationic amphiphile alone showed poor antibacterial activity, whereas nanostructures formed by co-assembling the complementary units showed significantly enhanced antibacterial efficiency. Further, the systematic variation of several structural parameters such as shape, spacing between the cationic groups and size of these nanostructures allowed us to elicit the role of each parameter on the overall antibacterial properties. Finally, we investigated the origin of the differing antibacterial activity of these nanoparticles having different shape and size but with the same molecular composition, by comparing the thermodynamic parameters of their binding interactions with a bacterial membrane mimic.