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Chitosan quaternary ammonium salt antibacterial agents with a single structure have the drawbacks of slow bactericidal speed and poor bactericidal effect, which cannot meet the practical usage requirements. To address the problem, in this study, we designed and synthesized a novel chitosan derivative containing double quaternary ammonium salt and chloride hydantoin structures (QCS-CA-DEADH-Cl) by using chitosan, 5,5-dimethyl hydantoin, methyl iodide, and 2-Dimethylaminoethyl chloride hydrochloride as the main raw materials, and then used as antibacterial agent. The structure of QCS-CA-DEADH-Cl was characterized by Fourier transform infrared spectra, X-ray photoelectron spectroscopy, Thermogravimetric, and Scanning electron microscopy. The antibacterial activity of QCS-CA-DEADH-Cl, and the renewability and stability of N-Cl structure in QCS-CA-DEADH-Cl were explored. The results indicated that the N-Cl structure of QCS-CA-DEADH-Cl has strong renewability and storage stability. Moreover, the synergistic effect of quaternary ammonium salt structure and N-Cl structure endowed QCS-CA-DEADH-Cl with excellent antibacterial activity. This work does not only provide a new perspective for the preparation of novel chitosan antibacterial agents but also contributes to expanding the comprehensive utilization of biomass resources.