Background and objective: Nosocomial infections following influenza are important causes of death, requiring early implementation of preventive measures, but predictors for nosocomial infection in the early stage remained undetermined. We aimed to determine risk factors that can help clinicians identify patients with high risk of nosocomial infection following influenza on admission. Method: Using a database prospectively collected through a Chinese national network for hospitalised severe influenza A(H1N1) pdm09 patients, we compared the characteristics on admission between patients with and without nosocomial infection. Result: A total of 2146 patients were enrolled in the final analysis with a median age of 36.0 years, male patients comprising 50.2% of the sample and 232 (10.8%) patients complicated with nosocomial infection. Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Staphylococcus aureus were the leading pathogens, and invasive fungal infection was found in 30 cases (12.9%). The in-hospital mortality was much higher in patients with nosocomial infection than those without (45.7% vs 11.8%, P < 0.001). Need for mechanical ventilation (OR: 3.336; 95% CI 2.362-4.712), sepsis (OR: 2.125; 95% CI 1.236-3.651), ICU admission on first day (OR: 2.074; 95% CI 1.425-3.019), lymphocytopenia (OR: 1.906; 95% CI 1.361-2.671), age > 65 years (OR: 1.83; 95% CI 1.04-3.21) and anaemia (OR: 1.39; 95% CI 1.39-2.79) were independently associated with nosocomial infection. Conclusion: Need for mechanical ventilation, sepsis, ICU admission on first day, lymphocytopenia, older age and anaemia were independent risk factors that can help clinicians identify severe influenza A(H1N1) pdm09 patients at high risk of nosocomial infection.