Background: Analyze the clinical characteristics of Mycoplasma pneumoniae pneumonia with hypoxia in children, and identify the related factors of hypoxia in MPP. Methods: A retrospective case-control study was performed on 345 children with Mycoplasma pneumoniae pneumonia (MPP) hospitalized in our hospital from January 2017 to June 2019. The clinical features, laboratory data and radiological findings were compared between the MPP with hypoxia, refractory Mycoplasma pneumoniae pneumonia (RMPP) and general Mycoplasma pneumoniae pneumonia (GMPP) groups. Results: MPP with hypoxia patients (n=69) had a higher incidence of extra-pulmonary complications and more serious radiological findings(P<0.05), besides the days of fever and in the hospitals were longer. And they also need more complicated treatments(P<0.05). Meanwhile, the levels of white blood cell count(WBC), C-reactive protein(CRP), lactic dehydrogenase (LDH), interleukin (IL)-6, ferritin, D-dimer, fibrinogen(FG), alanine aminotransferase(ALT) and the percentage of neutrophils in the MPP with hypoxia group were significantly higher than those in the RMPP group and the GMPP group (P<0.05). In ROC curve analysis, the percentage of neutrophils, WBC, CRP, LDH, IL-6, ferritin, D-dimer, and ALT were contributed to identify MPP with hypoxia patients. Multivariate logistic regression analysis showed that ferritin>174.15 ng/mL, IL-6>25.475pg/ml and pleural effusion had important effects on hypoxia in MPP (P<0.01).Conclusion: MPP with hypoxia patients presented more serious clinical manifestations. Ferritin>174.15 ng/mL, IL-6>25.475pg/ml and pleural effusion were related clinical factors for hypoxia in MPP.