Background During the COVID-19 pandemic, we continuously monitored the epidemiology of influenza virus among pediatric patients from January 2021 to December 2023 in Hainan Island, China. Methods In this study, we collected 54,974 nasopharyngeal swab samples for IAV testing and 53,151 samples for IBV testing from pediatric outpatients. Additionally, we also collected 19,687 nasopharyngeal swab samples from pediatric inpatients for IAV and IBV testing. Outpatient samples were screened for IVs infection by the colloidal gold method. Targeted Next-Generation Sequencing (tNGS) was used to detect Influenza virus infections in inpatients. Influenza virus types were identified by analyzing the HA/NA partial regions. Results The findings revealed a decrease in the infection rate of IBV over the specified period, while the infection rate of IAV exhibited a rising trend. Additionally, B/Victoria lineage was the dominant epidemic strain in 2021, while the epidemic strains in 2022 and 2023 underwent a dynamic transformation from A/H3N2 to A/H1N1. Phylogenetic analysis revealed close relationships among the circulating strains. Nonetheless, because the sample size is limited, additional research is required. Conclusion Our findings suggest that the predominant types of influenza viruses in the pediatric population are dynamically changing, and non-pharmaceutical intervention measures can significantly impact the infection rate of influenza.