Objective To determine the occurrence and independent risk factors of hypoxemia during one lung ventilation (OLV) before pleurotomy using short apnea combined with intraoperative pulmonary obstruction technique. Methods A total of 107 patients who underwent partial pulmonary resection were enrolled. According to the presence of hypoxemia from lung isolation and OLV to pleurotomy, they were divided into two groups: a hypoxemia group (group YH, n=24) and a non‑hypoxemia group (group NH, n=83). The incidence of hypoxemia was recorded, while the changes of arterial partial pressure of oxygen (PaO2) and arterial partial pressure of carbon dioxide (PaCO2) in patients with hypoxemia were observed before and 1 min after removal of intraoperative pulmonary obstruction. Multivariate logistic regression analysis was performed to determine the independent risk factors for hypoxemia before pleurotomy. Results Among the 107 patients, the incidence of hypoxemia before pleurotomy was 22.4%. For 14 patients with hypoxemia, the PaO2 before removal of intraoperative pulmonary obstruction was lower than that 1 min after the removal (P<0.05), without statistical difference (P>0.05). Multivariate logistic regression analysis showed that both the prolonged OLV‑pleurotomy time (OLV‑TE) [odds ratio (OR)=1.141, 95% confidence interval (CI) 1.043−1.249] and an increased peak airway pressure (Ppeak) during OLV (OR=1.235, 95%CI 1.035−1.473) were the independent risk factors for hypoxemia before pleurotomy. Conclusions The incidence of hypoxemia is 22.4% during OLV before pleurotomy through short apnea combined with intraoperative pulmonary obstruction technique, and both the prolonged OLV⁃TE and the increased Ppeak during OLV are the independent risk factors for hypoxemia before pleurotomy. Removal of intraoperative pulmonary obstruction is an effective method to correct hypoxemia before pleurotomy.