β-Thujaplicin possess a variety of biological activities. The use of modified biological nanoparticles (NPs) to develop novel anti-influenza drugs has increased in recent years. Selenium nanoparticles (SeNPs) with antiviral has attracted increasing attention for biomedical intervention. Functionalized SeNPs by β-Thujaplicin (Se@TP) surface modified with superior antiviral were synthesized in this study. β-Thujaplicin decoration of SeNPs obviously inhibited H1N1 infection and were less toxicity. Se@TP could inhibit H1N1 from infecting Madin Darby Canine Kidney (MDCK) cells and block chromatin condensation and DNA fragmentation. Se@TP obviously prevented MDCK cells from generating reactive oxygen species (ROS). Furthermore, Se@TP prevent lung injury in H1N1 infected mice through eosin staining and hematoxylin in vivo . Additionally, when treated with Se@TP, the DNA damage of lung tissues reduced substantially by TUNEL-DAPI test. Mechanistic investigation revealed that Se@TP inhibited H1N1 influenza virus from infecting MDCK cells through induction of apoptosis via suppression AKT and p53 signaling pathways through Immunohistochemical assay. Our results suggest that β-Thujaplicin modified SeNPs as carriers is an efficient way to achieve antiviral pharmaceutical candidate for H1N1 influenza.