Abstract Background: From January 24, 2020 to May 18, 2020, Chaoshan took measures to limit the spread of COVID-19, such as restricting public gatherings, wearing masks, and suspending classes. This study explored the effects of these measures on the pathogen spectrum of children in the Chaoshan area. Methods: Pharyngeal swab samples were collected from children hospitalized for respiratory tract infection. We used liquid chip technology to analyze 14 respiratory pathogens. Data were used to explore group differences, age related differences and seasonal variations in respiratory pathogens. Results: The study included 4075 children. The number of cases in the outbreak group (1222) was 42.8% of that in the pre-outbreak group (2853). The virus-detection rate was similar in the outbreak (48.3%, 590/1222) and pre-outbreak groups (51.5%, 1468/2853; χ2 = 3.446, P = 0.065), while the bacteria-detection rate was significantly lower in the outbreak group (26.2%, 320/1222) than in the pre-outbreak group (44.1%, 1258/2853; χ2 = 115.621, P < 0.05). With increase in age, the proportions of RSV and CMV infections gradually decreased, while those of MP, SP, and Adenovirus infections increased. SP, CMV, and Rhinovirus infections peaked in autumn and winter, while RSV infections peaked in summer and winter. Conclusion: Anti-COVID-19 measures significantly reduced the number of children hospitalized for respiratory tract infections, significantly altered the pathogen spectrum of respiratory tract infections, and decreased the overall detection rates of 14 common respiratory pathogens. The proportion of bacterial infections decreased, but that of viral infections did not.