Abstract: Objective This study aimed to characterize the nasopharyngeal microbiota in children with community-acquired pneumonia (CAP) across the spectrum from health status to infection subtypes and disease severity, providing a basis for the precise diagnosis and treatment as well as microecologically mechanistic understanding for CAP. Methods A total of 55 children with CAP were enrolled, including 37 cases of Mycoplasma pneumoniae (MP) infection (comprising 20 cases of simple MP infection and 17 cases of co-infection with MP and bacteria) and 18 cases of bacterial infection; in addition, 30 healthy children were enrolled as controls. Nasopharyngeal swab samples were collected and profiled using 16S rRNA gene sequencing to characterize the structure and composition of the nasopharyngeal microbiota. Differences were validated for robustness using statistical methods incorporating multifactor adjustments (for age, sex, and season). Results Children with CAP were significantly younger than healthy controls (P = 0.012), and there was a statistically significant difference in gender distribution between the two groups (P < 0.001). Children with CAP exhibited a dysbiotic nasopharyngeal microbiota characterized by a reduction of protective Corynebacterium (7.27% vs 9.81%, P = 0.033) and an enrichment of potentially pathogenic Prevotella (2.59% vs 0.12%, P = 0.008). The relative abundance of Prevotella was positively correlated with the number of clinical symptoms (r = 0.41, P < 0.001). Multivariate PERMANOVA analyses revealed that the overall structure of the nasopharyngeal microbiota differed significantly across infection subtypes and disease severity (P=0.012, P=0.042). However, after strict correction, no stable genus-level specific markers were identified. Conclusion This study revealed a progressive discriminative pattern of nasopharyngeal microbiota in children with CAP: core species biomarkers are identifiable at the disease-versus-health level, while at the levels of infection subtypes and disease severity, microbiota differences are primarily manifested as the restructuring of the overall community structure rather than genus-specific alterations, thus providing a "systems biology" perspective for understanding the microecological mechanisms of CAP and crucial theoretical groundwork for future exploration of developing microbial community structure as a discriminatory tool.