The bactericidal mechanisms of poly(phenylene ethynylene) (PPE)-based cationic conjugated polyelectrolytes (CPE) and oligophenylene ethynylenes (OPE) were investigated using electron/optical microscopy and small-angle X-ray scattering (SAXS). The ultrastructural analysis shows that polymeric PPE-Th can significantly remodel the bacterial outer membrane and/or the peptidoglycan layer, followed by the possible collapse of the bacterial cytoplasm membrane. In contrast, oligomeric end-only OPE (EO-OPE) possesses potent bacteriolysis activity, which efficiently disintegrates the bacterial cytoplasm membrane and induces the release of bacterial cell content. Using single giant vesicles and SAXS, we demonstrated that the membrane perturbation mechanism of EO-OPE against model bacterial membranes results from a 3D membrane phase transition or perturbation.