Objective To investigate the incidence of hypoxemia in the anesthesia recovery period after thoracoscopic surgery and explore the risk factors of hypoxemia and its predictive efficiency. Methods A total of 841 patients, aged 18‒90 years, American Society of Anesthesiologists (ASA) physical status of Ⅰ‒Ⅲ, who were scheduled for thoracoscopic surgery from October 2017 to May 2019 in the Second Affiliated Hospital of Zhejiang University School of Medicine, were retrospectively analyzed in the current study. They were divided into a hypoxemia group and a non‑hypoxemia group, according to the presence of hypoxemia in the anesthesia recovery period. Both groups were compared for their clinical data before and during surgery to evaluate the condition of hypoxemia in the recovery period. Their risk factors were analyzed by multivariate Logistic regression. A receiver operating characteristic (ROC) curve was established to examine its predictive efficiency towards hypoxemia. Results Among the 841 patients, 239 patients (28.4%) presented hypoxemia during the anesthesia recovery period. The risk factors of hypoxemia included age [odds ratio (OR)=1.028, 95% confidence interval (CI) 1.006‒1.050], body mass index (BMI) (OR=1.217, 95%CI 1.111‒1.333), hypertension (OR=2.462, 95%CI 1.564‒3.875), mediastinal surgery (OR=2.756, 95%CI 1.605‒6.873) and supine position (OR=2.230, 95%CI 0.936‒5.314). For hypoxemia in the anesthesia recovery period, its area under the receiver operating characteristic curve (AUC) was 0.723 (95%CI=0.685‒0.761, P<0.01), with a sensitivity of 63.6% and a specificity of 69.4%. Conclusions Extensive attention towards blood pressure control and body weight management before surgery, and comprehensive understanding the mechanism of hypoxemia caused by surgery at the supine position and active prevention, may reduce the incidence of hypoxemia during the anesthesia recovery period after thoracoscopic surgery.