To investigate the effect of positive end expiratory pressure (PEEP) level selection on prone position ventilation and inflammatory factors in patients with severe acute respiratory distress syndrome (ARDS). A prospective randomized controlled study was conducted. The 100 patients with severe ARDS admitted to Union Jiangbei Hospital, Huazhong University of Science and Technology from March 2016 to March 2019 were enrolled. Patients were divided into two groups according to the random number table method, with 50 cases in each group. All patients were given lung protective ventilation strategy and prone position ventilation treatment on the basis of treatment of primary disease. The lower level of PEEP [8-12 cmH2O (1 cmH2O = 0.098 kPa)] was the control group, and the higher level of PEEP (13-17 cmH2O) was the observation group. Patients' vital signs were continuously monitored during mechanical ventilation. The indexes of pulmonary recruitment were recorded, including the dynamic lung compliance (Cdyn), pulmonary drive pressure (DP), heart rate and lactate (Lac) levels before and 48 hours after the treatment. The levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), high sensitivity C-reaction protein (hs-CRP) in serum were detected by enzyme linked immunosorbent assay (ELISA). Arterial blood gas was detected, including arterial partial pressure of oxygen (PaO2), oxygenation index (PaO2/FiO2), and arterial partial pressure of carbon dioxide (PaCO2). The occurrence of pleural effusion and heart, liver and kidney dysfunction were recorded. In the control group, the PEEP level was (10.9±1.2) cmH2O, and the observation group PEEP level was (15.6±1.5) cmH2O. There was no significant difference in the index of lung recruitment, the levels of inflammatory factors and the arterial blood gas analysis index between the two groups before treatment. After prone ventilation, the index of lung recruitment and the arterial blood gas analysis index were much better in both groups. The effect of lung recruitment and oxygenation in the observation group with higher PEEP level were significantly superior to the control group with lower PEEP level [Cdyn (mL/cmH2O): 37.61±5.09 vs. 32.51±4.97, DP (cmH2O): 10.36±1.51 vs. 12.55±1.35, heart rate (bpm): 93.13±10.56 vs. 108.56±12.49, Lac (mmol/L): 2.34±0.41 vs. 3.41±0.57, PaO2 (mmHg, 1 mmHg = 0.133 kPa): 95.13±3.33 vs. 91.81±2.75, PaO2/FiO2 (mmHg): 180.12±7.25 vs. 150.29±8.52, PaCO2 (mmHg): 38.31±2.13 vs. 45.22±2.61, all P < 0.05]. The levels of inflammatory factors after treatment were higher than before treatment in both groups. Higher PEEP level will cause increased inflammatory factor level than the control group [IL-6 (ng/L): 526.24±125.18 vs. 465.18±130.52, TNF-α (ng/L): 42.47±2.20 vs. 34.12±1.89, hs-CRP (mg/L): 101.24±23.26 vs. 83.56±25.51, all P < 0.05]. Furthermore, the occurrence of pleural effusion and heart, liver, kidney dysfunction in the observation group were lower than that of the control group (4.0% vs. 8.0%, 10.0% vs. 16.0%, 2.0% vs. 10.0%, 2.0% vs. 6.0%, respectively, all P < 0.05). The higher PEEP level combined with prone position ventilation is beneficial to the severe ARDS patients with better lung recruitment effect and arterial blood gas improvement, thus promote the patients' recovery. But the higher initial PEEP will induce the release of inflammatory factors to a certain extent.