Pectobacterium carotovorum subsp. carotovorum (Pcc) was a pathogen that could cause serious soft rot disease of Chinese cabbage. In order to control Pcc, Athyrium sinense essential oil-loaded chitosan nanoparticles (AEO-loaded CSNPs) was obtained by embedding the Athyrium sinense essential oil (AEO) in chitosan nanoparticles (CSNPs) through ion gel method, and it was characterized and further evaluated for the antibacterial properties. The results of gas chromatography-mass spectrometer (GC-MS) analysis showed that the main components of AEO were n-hexadecanoic acid (32.18%), linoleic acid (18.28%), phytol (8.67%), fitone (4.79%), α-linolenyl alcohol (2.54%), isophytol (2.04%) and hexadecanoic acid methyl (2.03%). When chitosan (CS)/AEO ratio was 1:0.25, zeta potential was 25.7 mv, entrapment efficiency (EE) was 48.43% and loading capacity (LC) was 6.23%. These indices reached the maximum value, showing that ratio of 1:0.25 was the optimal condition for the preparation of AEO-loaded CSNPs. Therefore, AEO-loaded CSNPs prepared by using CS/AEO ratio of 1:0.25 was used for further characterization. The AEO-loaded CSNPs observed by atomic force microscopy exhibited regular shapes. Thermogravimetric analysis, fourier transform infrared, and X-ray diffraction results indicated that AEO-loaded CSNPs were effectively loaded with AEO and AEO-loaded CSNPs were successfully prepared. Finally, the antibacterial properties of AEO-loaded CSNPs were evaluated by MIC and MBC, in vitro release (within 48 h), time-kill curve (within 60 h) and in vivo experiments (within 72 h). The MIC and MBC of AEO-loaded CSNPs were 0.16 mg/mL and 0.63 mg/mL, respectively. The MIC and MBC results indicated that AEO-loaded CSNPs effectively enhanced the antibacterial activity of AEO. In vitro release results indicated that AEO-loaded CSNPs was consistent with the behavior of Fickian release and had the excellent release properties. Time-kill curve results indicated that AEO-loaded CSNPs had the characteristics of sustainability and stability. In vivo experiments (incubation for 72 h at 28 °C) showed that preventive and therapeutic effects of AEO-loaded CSNPs were 82.5% and 80.43%, which indicated that CSNP system effectively improved the in vivo effects of AEO. In conclusion, AEO-loaded CSNPs could be used as an effective antibacterial agent to control Pcc.