Background Flexible bronchoscopy has been favored for the diagnosis and treatment of respiratory diseases, but significant desaturation frequently occurs during bronchoscopy. Current guidelines do not provide a consensus about the optimal saturation target during bronchoscopy. Methods We performed a retrospective cohort study with propensity score matching in a single center including 569 patients who received bronchoscopy from March 1st,2020 to February 28th,2021. Patients were classified into high- or low-oxygen saturation groups according to the saturation of percutaneous oxygen (SpO2) during bronchoscopy. The primary outcome was post-bronchoscopy respiratory adverse events. Secondary outcomes were other post-bronchoscopy adverse events and clinical outcomes. Results We classified 458 patients into the high-oxygen saturation (SpO2 > 96%) group, and 111 into the low-oxygen saturation (SpO2 ≤ 94%) group (Fig. 1). Demographic and clinical features were similar between the two groups. Low-oxygen saturation group had significantly higher respiratory adverse events (p-value=0.001) and febrile events (p-value<0.001) (Table 1). However, there was no significant difference in hospital length of stay, intensive care unit admission, or 7-day-all-case mortality between the two groups. In multivariable regression analysis, low-oxygen saturation group was an independent risk factor for post-bronchoscopy respiratory adverse events (odds ratio=3.12 [95% confidence interval=1.19-8.16], p-value=0.020). Especially, the risk for post-bronchoscopy respiratory adverse events in the low-oxygen saturation group was significantly identified in subgroup patients who were ≥65 years old, female, current smokers, diagnosed with chronic obstructive pulmonary disease, and presenting acute decompensated heart failure before bronchoscopy (Fig. 2). Conclusions The patients showing SpO2 ≤ 94% during bronchoscopy should be closely monitored after bronchoscopy regarding the increased risk of developing adverse events.