Background: An increased number of refractory mycoplasma pneumoniae (MP) pneumonia (MPP) cases have been reported. However the duration of MP infection in lower airway and the course of anti-MP treatment remains unclear. Methods: We retrospectively reviewed the medical records of 94 MPP children. Patients were classified into two groups. The long-term group (Group LT) was defined as bronchoalveolar lavage fluid (BALF) remained MP-positive by PCR after 30 days of the disease course. The non-long-term group (Group NLT) was defined as BALF became MP-negative by PCR within 30 days of disease and patients who only needed one bronchoscopy lavage therapy. MP loads, clinical outcomes were analyzed along with other clinical measurements. Results: The average levels of inflammatory markers such as C reactive protein and lactate dehydrogenase in Group LT were significantly higher than those in Group NLT. Airway and lung damage in Group LT were more severe than Group NLT. 28 patients developed necrotizing pneumonia and 8 patients developed pulmonary embolism in Group LT. Mean maximum MP loads in BALF were 107.46 ± 0.93 and 104.86 ± 0.93 in Groups LT and NLT, respectively. There was persistent MP DNA in Group LT, even lasted for 120 days. One severe MPP patient in Group LT had MP-associated bloodstream infection. After 3 months of follow-up, chest imaging revealed incomplete absorption of pulmonary consolidation in 33 patients of Group LT [including 13 airway obliterans (AO) patients] and in 7 patients of Group NLT (including 2 AO patients). Conclusion: MP loads of BALF were associated with the subsequent duration of MP DNA in lower airway. High MP loads and persistent long-term MP DNA in lower airway were associated with severity of pediatric MPP. © 2019 The Author(s).