Developing biodegradable cationic polymers with high antibacterial efficiency and low cytotoxicity is of great significance in biological applications. Selenium is an essential trace element for the human body, and selenium-containing compounds are promising in various health-related applications. To combine selenium with biodegradability, selenide-functionalized polycaprolactones (PCL) with different hydrophobic substituents were synthesized followed by selenoniumization. The optimal polyselenonium salt showed excellent antibacterial activity with an MBC of 2 μg mL-1 and an MIC of 1 μg mL-1 and exhibited good biocompatibility before and after degradation. In addition, the obtained selenium polymer can be well blended with commercial PCL by electrospinning, and films with good antibacterial activity were prepared. This work enriches the knowledge of selenium derivatives and lays a foundation for follow-up research on selenium cationic polymers in the antimicrobial field.