BACKGROUND: To characterize the epidemiology of pathogens in children with lower respiratory tract infections (LRTI) using targeted next-generation sequencing (tNGS), assess the correlation between reads per ten million (RPTM) of co-detected pathogens, identify common co-detection patterns, and explore their clinical significance. METHODS: Children aged 29 days to 14 years hospitalized for LRTI at the Department of Pediatrics, Zhongnan Hospital of Wuhan University, from April 2023 to August 2024 were included. Bronchoalveolar lavage fluid (BALF) or nasopharyngeal swab (NS) samples were tested for pathogens using tNGS, and clinical data were collected. The data and RPTM were statistically analyzed based on lung X-ray and CT scan results, classifying cases as pneumonia or lung consolidation/pulmonary atelectasis (LC/PA). RESULTS: Among 1118 children, the highest pathogen detection rate was Mycoplasma pneumoniae (MP) at 60.20%, followed by Haemophilus influenzae (HI) at 42.40% and Streptococcus pneumoniae (SP) at 35.42%. In children under 4 years old, common pathogens were HI, Rhinovirus (RhV), and Respiratory syncytial virus (RSV). For those over 4 years old, MP and HI were predominant. In common pneumonia cases, MP, HI, and RhV were frequent, with MP being the primary pathogen in LC/PA. 80.70% of respiratory samples detected two or more pathogens, and viruses were more frequently detected in NS than in BALF. Correlation analysis showed that MP RPTM was negatively correlated with other co-detected pathogens' RPTM, SP was negatively correlated with RSV but positively correlated with Influenza virus (flu virus), HI was positively correlated with Adenovirus (ADV) and flu virus, RhV was negatively correlated with flu virus. Clinical characteristics of co-detected pathogens showed no significant differences in acute LRTI symptoms among different combinations. CONCLUSION: Co-detection of pathogens in children's LRTI using tNGS was common, with MP and bacterial infections being predominant. There were synergistic and competitive relationships between the RPTM of co-detected pathogens.