Emerging studies have demonstrated the importance of microbial topography for upper respiratory tract (URT) niches in respiratory health. Nonetheless, the microbial topography between nasopharyngeal (NP) and oropharyngeal (OP) microbiota remains to be understood for pediatric pneumonia. This study recruited 119 Chinese children (59 healthy controls and 60 pneumonia patients) to analyze the association of pneumonia with the similarity between NP and OP microbiota. Children in the control group had more notable URT microbial topography than in the pneumonia group. In addition, higher similarity between NP and OP microbiota was identified in high-severity patients when compared to low-severity ones. Further analysis found that the compromised microbial topography was mainly driven by Staphylococcus. Our data suggest the role of translocation between NP and OP microbial communities in the development of pediatric pneumonia.