To investigate the effect of inverse ratio ventilation (IRV) combined with positive end-expiratory pressure (PEEP) in infants undergoing thoracoscopic surgery with single lung ventilation (OLV) for lung cystadenomas. A total of 66 infants undergoing thoracoscopic surgery with OLV for lung cystadenomas in our hospital from February, 2018 to February, 2019 were randomized into conventional ventilation groups (group N, n=33) and inverse ventilation group (group R, n=33). Hemodynamics and respiratory parameters of the infants were recorded and arterial blood gas analysis was performed at 15 min after two lung ventilation (TLV) (T1), OLV30 min (T2), OLV60 min (T3), and 15 min after recovery of TLV (T4). Bronchoalveolar lavage fluid was collected before and after surgery to detect the expression level of advanced glycation end product receptor (RAGE). Sixty-three infants were finally included in this study. At T2 and T3, Cdyn, PaO2 and OI in group R were significantly higher (P < 0.05) and Ppeak, PaCO2 and PA-aO2 were significantly lower than those in group N (P < 0.05). There was no significant difference in HR or MAP between the two groups at T2 and T3 (P > 0.05). The level of RAGE significantly increased after the surgery in both groups (P < 0.05), and was significantly lower in R group than in N group (P < 0.05). In infants undergoing thoracoscopic surgery with OLV for pulmonary cystadenoma, appropriate IRV combined with PEEP does not affect hemodynamic stability and can increases pulmonary compliance, reduce the peak pressure, and improve oxygenation to provide pulmonary protection.