Objective To compare the effects of individualized positive end-expiratory pressure (PEEP) and fixed PEEP on postoperative pulmonary complications (PPCs) in thoracic surgery by systematic evaluation. Methods A computerized search of PubMed, Cochrane Library, Embase, China Knowledge, Wanfang, and Wipro databases was conducted to collect randomized controlled trials (RCTs) of the intraoperative use of individualized PEEP and immobilized PEEP in thoracic surgery, and the literature was searched from the establishment of each database to December 2023. Meta-analysis was performed using RevMan 5.4 software after literature screening, data extraction, and quality assessment by at least 2 researchers independently following the Cochrane Handbook. Results A total of 13 RCTs were included, with a total of 3535 patients, 1775 in the individualized PEEP group and 1760 in the control group. Compared with the control group, the incidence of postoperative pulmonary complications was significantly lower in the individualized PEEP group (OR=0.38,95%CI0.29-0.51,P0.00001), intraoperative PaO2 was significantly higher (SMD=0.27,95%CI0.12-0.42,P=0.0005), and intraoperative pulmonary compliance was significantly higher (SMD=0.75,95%CI0.67～0.82,P＜0.00001), and intraoperative driving pressure was significantly lower (SMD=-2.17,95%CI-2.42～-1.93,P＜0.00001). There was no statistically significant difference in intraoperative MAP and postoperative hospitalization time between the two groups. Conclusion Compared with fixed PEEP, the use of individualized PEEP in thoracic surgery can improve intraoperative oxygenation, increase pulmonary compliance, reduce driving pressure, and decrease the incidence of postoperative pulmonary complications.