Thise study is aimed to identify the biomarkers for predicting refractory Mycoplasma pneumoniae pneumonia in Chinese children at the time of the hospital admission. The case control study retrospectively analyzed the clinical characteristics and laboratory results of Chinese pediatric patients presenting with common and refractory Mycoplasma pneumoniae pneumonia (CMPP and RMPP). Overall, there were 216 cases in the CMPP group and 88 cases in the RMPP group. Venous blood was collected, and serum ferritin (SF), lactate dehydrogenase (LDH), D-dimer, C-reactive protein (CRP), procalcitonin (PCT), neutrophil count/lymphocyte count (NLR), and other indexes were measured. A single factor analysis, an ROC curve analysis, and a logistic regression analysis were used to determine the independent risk factors of RMPP and find combination of initial markers for RMPP. There were significant differences between the RMPP group and the CMPP group in mean SF (529.82 357.86 vs. 147.22 122.68 ng/mL), LDH (522.08 389.08 vs. 286.85 101.02 U/L), D-dimer (6.65 5.66 vs. 1.46 2.45 μg/mL), CRP (62.80 52.15 vs. 19.03 24.50 mg/L), PCT (0.80 2.61 vs. 0.16 0.44) ng/mL, and NLR (4.14 2.52 vs. 2.62 1.55), with P < 0.05 for each comparison. ROC cut-off values of the above indexes were 329.01 ng/mL, 375.50 U/L, 2.10 μg/mL, 43.08 mg/L, 0.08 ng/mL, and 2.96, respectively. The logistic regression analysis showed that SF, D-dimer, and CRP are independent risk factors to predict RMPP. SF, D-dimer, and CRP are statistically significant biomarkers to predict RMPP in Chinese children patients in the settings of pediatric emergency department.