Background: To analyze the relationship between granulocyte-macrophage colony-stimulating factor (GM-CSF) and high mobility group box 1 (HMGB1) level in alveolar lavage fluid with the clinical characteristics and prognosis of children refractory mycoplasma pneumoniae pneumonia (MPP), so as to provide reliable targets for clinical diagnosis and treatment. Methods: A total of 106 children diagnosed with MPP and prepared for bronchoalveolar lavage therapy were selected in this study, which were divided into 2 groups according to clinical diagnosis: those showing clinical and radiological deterioration despite appropriate antibiotic therapy for ≥7 days were classified into refractory MPP group (n=47), while the others were classified into non-refractory MPP group (n=59). The data of physical examination, treatment and outcome were collected. In addition, the GM-CSF and HMGB1 levels in alveolar lavage fluid during each bronchoalveolar lavage therapy were detected by ELISA kits. Results: There was no significant difference in age, sex, course of fever, the highest temperature, WBC, L, PLT, ALT, AST, CK-MB, D-D, CK, IgG, IgA, IgM, C3, and C4 between refractory MMP group and non-refractory MMP group on admission (P>0.05). The levels of N, CRP, PCT, and LDH in refractory MPP group were higher than those in non-refractory MPP group, the difference had statistical significance (P<0.05). Both GM-CSF and HMGB1 levels were positively correlated with traditional indicators N, CRP, PCT and LDH (r=0.611-0.785, P<0.05). ROC analysis results showed that CRP, GM-CSF and HMGB1 had predictive value for refractory MPP attack (AUC=0.636, 0.657, 0.651, P<0.05). Logistic regression analysis results showed GM-CSF and HMGB1 were independent factors for refractory MPP (B>1.0, P<0.05). ROC analysis results showed that GM-CSF and HMGB1 at 2nd bronchoalveolar lavage therapy had predictive value for long hospital stay (>28 d) and poor prognosis of refractory MPP (AUC=0.782-0.825, P < 0.05). Conclusion: The level of GM-CSF and HMGB1 in alveolar lavage fluid is closely related to the occurrence and development of refractory MPP, which can be used as an auxiliary indicator for clinical diagnosis and prognosis evaluation, and has certain guiding significance for its clinical treatment.