Objective: Following the outbreak of the novel coronavirus pandemic, a series of preventive and control measures were adopted by the public, which have had a certain impact on the occurrence of respiratory infectious diseases and changes in their etiology. This article aims to explore the changes in respiratory pathogens among children with respiratory infections during the COVID-19 pandemic and after the comprehensive lifting of restrictions, providing a basis for the clinical diagnosis and treatment of pediatric respiratory infections in the post-pandemic era. Methods: We retrospectively reviewed and analyzed the targeted sequencing results of multiple respiratory pathogens in children with respiratory infections treated at the Children’s Hospital affiliated with Shandong University from January 2022 to December 2023. Results: A total of 16,571 targeted sequencing results of pathogens from children with respiratory infections were included in the analysis (2,810 cases in 2022 and 13,761 cases in 2023). The overall positive detection rates of pathogens in 2022 and 2023 were 95.19% and 96.56%, respectively. The positive detection rates for single pathogens were 16.01% vs. 19.29%, while the rates for two or more pathogens were 79.18% vs. 77.27%. The top three viral pathogens with the highest positive detection rates in both 2022 and 2023 were rhinovirus, parainfluenza virus, and respiratory syncytial virus. In 2023, the top three bacterial pathogens were Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus, whereas in 2022, they were Streptococcus pneumoniae, Haemophilus influenzae, and Bordetella pertussis. The positive detection rates of Haemophilus influenzae, Staphylococcus aureus, Mycoplasma pneumoniae, respiratory syncytial virus, adenovirus, influenza A virus, and rhinovirus in 2023 were significantly higher than those in 2022 (all P < 0.05). However, the positive detection rates of Streptococcus pneumoniae, Bordetella pertussis, and parainfluenza virus were significantly lower in 2023 than in 2022 (all P < 0.001). Differences in the positive detection rates of respiratory pathogens were observed across different age groups. Conclusion: Significant changes in the prevalence of certain pathogens occurred during the COVID-19 pandemic and after the lifting of restrictions. It is essential to strengthen long-term monitoring of common respiratory infectious diseases to guide early clinical intervention.