Objective To evaluate the genetic variation and trends of Influenza A H1N1 virus and to provide a theoretical basis for the prevention and control of influenza by analysis of gene detection of influenza a H1N1 virus. Methods Samples came from epithelial cells and secretions of patients with nasopharyngeal. Nucleic acid was extracted by the nucleic acid separation and purification system with 200μl sample. The amplification curve was analyzed by light cycler 480 PCR. The M gene, NP gene, HA gene and RNase P gene for each specimens were detected. When M gene, NP gene, HA gene, RNase P gene were positive, results were true positive. When HA gene was negative and the other three genes were positive, results were probable positive. Results Among detected 3673 samples, 2404 samples were negative and 1269 samples were positive of influenza A. The positive rate was 34.5%. 641 samples were positive of seasonal influenza, accounting for 50.5%. 628 samples were influenza A H1N1, accounting for 49.5%. 433 samples (68.9%) were true positive and 195 samples (31.1%) were probable positive. The peak of detection was in October for Influenza A H1N1, in September and December for a seasonal stream. The positive rate was 57.5% for young people, 39.9% for children aged, and only 2.6% for 60 or older. Conclusion Samples of Influenza A H1N1 are positive in M, HA, NP and RNaesP four genes. The peak of detection is in October, and infected people are mainly young and children.