Two sets of cationic surfactants each with essentially the same alkyl chains but different headgroup structures were studied to investigate the effects of surfactant headgroup structure on micelle microstructures, drag reduction (DR) and rheological properties at certain counterion and surfactant concentrations. Cetyldimethylethylammonium bromide (CDMEAB) was compared with alkyltrimethyl ammonium bromide (CnTAB) and benzyldimethyl(hydrogenated tallow)ammonium chloride (DMHTB) was compared with alkyltrimethylammonium chloride (CmTAC), respectively. Surfactants with larger headgroups showed lower high temperature limits for DR. CDMEAB systems have better DR abilities than CnTAB below room temperature but the opposite is true at higher temperatures. DMHTB has stronger counterion binding ability than CmTAC, giving better DR properties than CmTAC at low counterion concentration, but has a lower upper temperature limit for DR. These results provide further understanding of the self-assembly nature of threadlike micelles of cationic surfactants and guidance for design of effective surfactant structures to meet particular DR requirements.