Objective:To study the molecular mechanism of Maxing Shigan decoction in the treatment of H1N1 influenza A:by establishing molecular networks and comparing canonical pathways. Method: Target proteins of Maxing Shigan decoction and related genes of H1N1 influenza A were searched based on Pubchem and Gene databases on line. Molecular networks and canonical pathways comparison analyses were performed by Ingenuity pathway Analysis(IPA). Result: There were 186 targets proteins of Maxing Shigan decoction and 7 related genes of H1N1 influenza A. The molecular networks of Maxing Shigan decoction and H1N1 influenza A were multifunction. There were four cellular immune related pathways in all eight common pathways including:role of pattern recognition receptors in recognition of viruses

interlewkin 12(IL-12) signaling and production in macrophages

role of proten kinase(PKR) in interferon induction and antiviral response and Tumor necrosis factor receptor 1(TNFR1) signaling.Maxing Shigan decoction could regulate Toll-like receptor(TLR9)

phosphoinostide 3 -kinase(PI3K)

nucleotide-binding oligomerization domain 2(NOD2) and other molecules of cellular immune related pathways. Conclusion: Regulating many effective nodes of cellular immune related pathways maybe the way of Maxing Shigan decoction against H1N1 influenza A.