Objective To analysis the laboratory indicators of 208 cases with influenza A H1N1 and explore the characteristics and the value of laboratory indicators for the diagnosis and progression of the disease. Method The function of liver and kidney, T lymphocyte subsets and other laboratory indicators were detected in the course of disease. The backward summary and statistics analysis were performed. Results In the early stage, the counts of red blood cell and platelet in most patients were within the normal range. The counts of white blood cell in 43.3% of the patients decreased. The counts of neutrophils decreased in 36.1% and lymphocytes in 16.8% of the patients. The functions of liver and kidney in majority of patients were normal, and some of the patients showed electrolyte imbalance. CD3+, CD4+, CD8+ T lymphocytes significantly decreased, especially in critical patients. CD3+, CD4+, CD8+ T lymphocytes were extremely low in a few days after admission and recovery period with the improved condition. Conclusion The count of CD3+, CD4+, CD8+ T lymphocytes and peripheral blood lymphocytes should be the important indicators for early diagnosis and disease severity of influenza A H1N1 and have guiding value for progression and evaluation for curative efficiency and prognosis to dynamically observe the changes of the disease in the patients with H1N1 influenza.