Background: The present study aims to evaluate the influence of alveolar recruitment strategy (ARS) and positive end-expiratory pressure (PEEP) combined with autoflow on respiratory mechanics, the oxygen index (OI), pulmonary shut [Qs/Qt(%)], and the concentrations of IL-6 and TNF-α in venous blood after surgery in obese patients who experienced thoracic surgery with one-lung ventilation (OLV). Methods: A total of 36 obese patients with ASAII-III degree, who experienced selective pulmonary lobectomy, were within 36-74 years old, and had a BMI of 30-40 kg/m 2 , were randomly divided into two groups: control group (C group) and protective ventilation group (P group). In the P group, ARS was given once when OLV began. Then, ventilation at 7 mmHg of PEEP and autoflow were given. The P peak before OLV (T 1 ), at 30 minutes after OLV (T 2 ), and at the 5 minutes after two-lung ventilation (TLV) (T 3 ), and the changes of P plat and Cdyn were recorded. Then, arteriovenous blood was drawn at T 1 , T 2 , T 3 and T 4 (6 hours after the operation), blood-gas indicators, including SPO 2 , PaCO 2 and PaO 2 , were measured, and the value of Qs/Qt(%) was calculated. Afterwards, venous blood was collected at T 1 and T 5 (18 hours after surgery), and the concentrations of IL-6 and TNF-α were detected. The clinical pulmonary infection score (CPIS) was determined at the first day and seventh day after the operation.Results: In both groups, Cdyn and OI decreased, while P plat , P peak and Qs/Qt(%) increased (P<0.05) at T 2 , when compared with those at T 1 . At T 2 and T 3 , P plat and P peak decreased (P<0.05) in the P group, when compared with the C group. At T 2 , T 3 and T 4 , OI increased (P<0.05) in the P group, when compared with the C group. At T 2 , T 3 and T 4 , PaCO 2 and Qs/Qt(%) decreased in the P group, when compared with the C group. The concentrations of IL-6 and TNF-α decreased in the P group, when compared with the C group. Conclusions: The ventilation model of ARS and PEEP combined with autoflow can better reduce airway pressure and the production of injurious inflammatory cytokines in blood in obese patients. Furthermore, it can reduce Qs/Qt during and at 6 hours after thoracotomy, improve OI and maintain the acid-base balance of the internal environment, which may be applied in clinical work. This brings new enlightenment and needs to be clarified through further studies.