Objective To study the characteristics of bronchoalveolar lavage fluid (BALF) microbial distribution at different stages of refractory Mycoplasma pneumoniae pneumonia (RMPP) in children and its relationship with immune function. Methods A total of 108 children with RMPP were enrolled. The relative abundance, richness, and diversity of BALF microbiota, as well as immune function, were compared between the acute phase (n=61) and recovery phase (n=47). The correlations between the richness and diversity of BALF microbiota and immune function were analyzed. Results The relative abundance of Propionibacterium, as well as the Simpson index, Shannon index, Chao1 index, and Observed species index of BALF microbiota in the acute phase were significantly lower than those in the recovery phase (P<0.05). The relative abundances of Streptococcus and Prevotella, as well as the levels of complement C3, complement C4, immunoglobulin A (IgA), immunoglobulin G (IgG), and immunoglobulin M (IgM), were significantly higher in the acute phase than in the recovery phase (P<0.05). Simpson, Shannon, Chao1, and Observed species indices were negatively correlated with levels of complement C3, complement C4, IgA, IgM, and IgG (P<0.05). Conclusions In children with RMPP, the relative abundance of Propionibacterium and the richness and diversity of BALF microbiota in the acute phase are lower than those in the recovery phase, while the relative abundances of Streptococcus and Prevotella are higher in the acute phase. Microbial richness and diversity are closely related to immune function.