Influenza viruses cause significant morbidity and mortality in humans through epidemics or pandemics. The lack of effective therapeutical treatment underlines the importance of research for new antiviral compounds. Flavonoids widely exist in the plant kingdom, and their antiviral activities against various viruses have been recently reported. In this study, the anti-influenza A/WS/33 virus of quercetin 3-rhamnoside (Q3R) from Houttuynia cordata was evaluated using a cytopathic effect (CPE) reduction method, the assay results demonstrated that Q3R possessed strong anti-influenza A/WS/33 virus reducing the formation of a visible CPE. Q3R also did inhibit virus replication in the initial stage of virus infection by indirect interaction with virus particles. However, oseltamivir has relative weaker efficacy compared to Q3R. Therefore, these findings provide important information for the utilization of Q3R for influenza treatment.