Influenza virus is a RNA virus which causes human and animals to suffer influenza, leading to acute upper respiratory tract infection. The existing vaccines and drugs have limited role in the treatment of influenza virus subtype H1N1. We prepared the small interfering RNA targeting RNA polymerase (PA) gene of influenza A (H1N1) virus and studied its effect of inhibiting virus replication. We designed and synthesized three pairs of siRNA targeting PA gene of influenza A (H1N1) virus, as well as constructed expression plasmid pS-PA646, pS-PA841 and pS-PA1537, being transfected into MDCK cells and chicken embryos respectively and infected with influenza virus subtype H1N1, to detect effects of siRNA on inhibiting influenza virus replication. We conducted viral HA titer determination, real-time RT-PCR. The results show that in the designed 3 pairs of siRNA, pS-PA1537 can inhibit the replication of influenza A (H1N1) virus in MDCK cells and chicken embryos, laying the foundation for the development of therapeutic agents resistant H1N1.