Objective To explore the effects applying high flow nasal cannula (HFNC) oxygen therapy during bronchoalveolar lavage in children with refractory Mycoplasma pneumoniae pneumonia (MMP), and to provide providing a reference for selecting appropriate oxygen therapy during pediatric bronchoscopy. Methods A total of 86 children with refractory MMP scheduled for bronchoalveolar lavage were selected as research subjects and assigned to the HFNC group and the conventional group according the sequence of medical order with 43 cases in each. During the procedure, the HFNC group received HFNC oxygen therapy with a flow rate of 20-50 L/min and an oxygen concentration of 40%, while the conventional group received oxygen via nasal cannula at a flow rate of 4 L/min. The oxygen therapy effects and occurrence of adverse reactions were observed in both groups. Results Both groups successfully completed the examination. The incidence rate and duration of intraoperative hypoxemia in the HFNC group were significantly lower than those in the conventional group (both P<0.05). Comparisons of the lowest transcutaneous oxygen saturation and maximum respiratory rate at different time points showed statistically significant differences (both P<0.05). There were no significant differences between the two groups in terms of maximum heart rate, time taken for bronchoscopy, interruption rates due to hypoxia, and occurrence of intraoperative adverse events (all P>0.05). Conclusion HFNC oxygen therapy facilitates the smooth performance of bronchoalveolar lavage in children with refractory MMP, reduces the incidence of hypoxemia, and has good safety performance.