In recent years, nanotechnology has received more and more attention in the antiviral field. Among them, selenium nanoparticles (SeNPs) have received a lot of attention. Chitosan, as a substance with antiviral effect, is limited by water solubility, low bioavailability, and poor stability. In this study, the combination of SeNPs with chitosan (Se@CS) showed less toxic and good anti-H3N2 infection effect. CCK-8 and RT-PCR showed that Se@CS effectively prevented H3N2 infection of MDCK cells by inhibiting viral replication and preventing cell fragmentation and cell aggregation. In addition, Se@ CS can inhibit the excessive production of ROS and the change of mitochondrial membrane potential. More importantly, Se@CS can inhibit the late apoptosis of cells caused by virus, which may be related to the inhibition of apoptotic proteins in the ROS/JNK apoptotic signaling pathway. Finally, Se@CS was also found to inhibit H3N2induced inflammation and alleviate infection. These results prove that Se@CS is a promising inhibitor for controlling influenza H3N2 virus infection.