Thermoplastic polyurethanes (TPUs) are one of the most appealing materials with extensive applications in biomedical fields due to their versatile mechanical properties and excellent biocompatibility. In response to the escalating challenges of bacterial infections, it is desirable to obtain TPUs with intrinsic antibacterial activity, particularly for application in biomedical devices and public places. Herein, a cationic main-/side-chain structure regulation strategy in the TPU hard segment was adopted to introduce and optimize the antibacterial activity. This was achieved by synthesizing two types of quaternary ammonium salts (QAS)-containing chain extenders, i.e., N-methyl-N-alkyl-N,N-bis(2-hydroxyethyl) ammonium bromide (Mn, where n represents the N-alkyl chain length) and N,N-dimethyl-N-alkyl-N-2,3-propylene glycol (Dn), from N-methyldiethanolamine (MDEA) and 3-dimethylamino-1,2-propanediol (DMAD), respectively. Given the structural differences between Mn and Dn, main-chain-type PU-Mn and side-chain-type PU-Dn were subsequently obtained with QAS groups in the hard segment. The N-alkyl chain length, QAS content, and main-/side-chain types were systematically investigated to optimize bactericidal properties. The results revealed that a long N-alkyl chain (from C6 to C14) increased the antibacterial activity of the chain extenders and corresponding TPU films. Besides, side-chain-type PU-Dn films showed higher contact-active antibacterial activity than that exerted by the main-chain-type PU-Mn films. Remarkably, almost 100% of Staphylococcus aureus(S. aureus) could be killed by the PU-D14 film with a low QAS content (1.6 wt %). All the TPUs showed good thermal stability with a degradation temperature of 5% mass loss (Td,5%) above 300 °C. Moreover, the TPU films displayed excellent mechanical properties with the tensile strength at break varying from 20.7 to 47.5 MPa and ultimate elongation above 1000%. All of the intrinsic antibacterial films showed negligible hemolytic activities.