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Background We conducted a pathogenic analysis in the bronchoalveolar lavage fluid (BALF) samples from refractory Mycoplasma pneumoniae pneumonia (RMPP) children. Methods A total of 150 BALF samples from 60 RMPP patients were analyzed to investigate pathogenic changes. The characteristics of M. pneumoniae were analyzed through culture, real-time PCR, genotyping, antimicrobial susceptibility testing and proteomics. The other pathogens were determined using culture, sequencing and nucleic acid detection. Results In 60 RMPP cases, the bacteri