This study investigates the molecular epidemiology of *Mycoplasma pneumoniae* (M. pneumoniae) pneumonia in children in Wuhan, China, from October 2020 to March 2022. The main findings include: 1. **Epidemiological Characteristics**: Among 1,259 clinical samples, 461 (36.6%) were positive for M. pneumoniae via qPCR. Preschoolers (81.4%) were the most affected, with symptoms including fever, cough, and wheezing. The infection was more severe in school-age children aged 6-11 years. 2. **Genotype Analysis**: Metagenomic sequencing identified 127 samples with adhesin P1 genotypes, with P1-type 1 (88.98%) being the dominant genotype. No significant difference in pathogenicity was observed among different genotypes. 3. **Macrolide Resistance**: The macrolide resistance rate was 96%, with all mutations being A2063G in the 23S rRNA gene. There was no significant difference in the upper respiratory microbiome between patients with mild and severe symptoms. 4. **Clinical Manifestations and Severity**: Serological testing, particularly IgM titers exceeding 1:160, may serve as indicators for predicting severe cases. However, no specific genotype was associated with more severe clinical symptoms. 5. **Conclusion**: The study provides a foundation for understanding the epidemic and genomic features of M. pneumoniae in Wuhan post-COVID-19. Key findings include the efficacy of qPCR in detecting M. pneumoniae, the potential of high IgM titers as indicators for severity, and the lack of a direct correlation between disease severity and genotypic characteristics or respiratory microenvironment. The high prevalence of macrolide resistance mutations highlights the need for continued surveillance and novel therapeutic approaches.This study investigates the molecular epidemiology of *Mycoplasma pneumoniae* (M. pneumoniae) pneumonia in children in Wuhan, China, from October 2020 to March 2022. The main findings include: 1. **Epidemiological Characteristics**: Among 1,259 clinical samples, 461 (36.6%) were positive for M. pneumoniae via qPCR. Preschoolers (81.4%) were the most affected, with symptoms including fever, cough, and wheezing. The infection was more severe in school-age children aged 6-11 years. 2. **Genotype Analysis**: Metagenomic sequencing identified 127 samples with adhesin P1 genotypes, with P1-type 1 (88.98%) being the dominant genotype. No significant difference in pathogenicity was observed among different genotypes. 3. **Macrolide Resistance**: The macrolide resistance rate was 96%, with all mutations being A2063G in the 23S rRNA gene. There was no significant difference in the upper respiratory microbiome between patients with mild and severe symptoms. 4. **Clinical Manifestations and Severity**: Serological testing, particularly IgM titers exceeding 1:160, may serve as indicators for predicting severe cases. However, no specific genotype was associated with more severe clinical symptoms. 5. **Conclusion**: The study provides a foundation for understanding the epidemic and genomic features of M. pneumoniae in Wuhan post-COVID-19. Key findings include the efficacy of qPCR in detecting M. pneumoniae, the potential of high IgM titers as indicators for severity, and the lack of a direct correlation between disease severity and genotypic characteristics or respiratory microenvironment. The high prevalence of macrolide resistance mutations highlights the need for continued surveillance and novel therapeutic approaches.