Abstract An outbreak of influenza A virus subtype H1N1, also known as swine flu, in Mexico was occurred in April 2009. To design drugs for treating this epidemic is urgency. In this study, we employed the new sequences (2009) to build the N1 simulation structure by homology modeling, which has been checked for high reliability by Verify Score and Ramachandran plot. The latest H1 homology model was employed from Chen's report. 365,602 compounds from NCI database have been screened by docking study of H1 and N1, respectively. And then, nine candidates were screened and suggested as potent dual target candidates from the docking studies. In our investigation, drug resistance was found by our molecular simulation in the new N1 modeling structure to oseltamivir. However, the mechanism is still not clear; further clinical investigations are urgently required.