Background Patients with H7N9 avian flu concurrent with severe acute respiratory distress syndrome (ARDS) usually have a poor clinical outcome. Prone position ventilation (PPV) has been shown to improve the prognosis of patients with severe ARDS. This study explored the effects of PPV on the respiratory and circulatory mechanics of H7N9-infected patients with severe ARDS. Methods Individuals admitted to four hospitals designated for H7N9 patients in Guangdong province were treated with PPV, and their clinical data were recorded before and after receiving PPV. Results Six of 20 critically ill patients in the ICU received PPV. After treatment with 35 PPV sessions, the oxygenation index (OI) values of the six patients when measured post-PPV and post-supine position ventilation (SPV) were significantly higher than those measured pre-PPV (P < 0.05). The six patients showed no significant differences in their values for respiratory rate (RR), peak inspiratory pressure (PIP), tidal volume (TV) or arterial partial pressure of carbon dioxide (PaCO2) when compared pre-PPV, post-PPV, and post-SPV. Additionally, there were no significant differences in the mean values for arterial pressure (MAP), cardiac index (CI), central venous pressure (CVP), heart rate (HR), lactic acid (LAC) levels or the doses of norepinephrine (NE) administered when compared pre-PPV, post-PPV, and post-SPV. Conclusion PPV provided improved oxygenation that was sustained after returning to a supine position, and resulted in decreased carbon dioxide retention. PPV can thus serve as an alternative lung protective ventilation strategy for use in patients with H7N9 avian flu concurrent with severe ARDS.