Background To assess the impact of disinfection measures on the incidence of common diseases in children welfare institute during the epidemic of Corona Virus Disease 2019 (COVID-19), and provide a basis for the daily disinfection management of children welfare institute. Methods This study surveyed and analyzed common diseases among children under the age of 14 in one social children welfare institute in Shanxi Province from January to May in 2018–2020 by the year-on-year method. Results The prevalence rate of respiratory diseases in 2020 was a significantly negative growth compared with 2018 and 2019. There was no obvious pattern of changes in digestive diseases group. Conclusion In view of the above anti-epidemic measures, it indicates that the children gathering institutions should strengthen effective personal protection and public health management to reduce infectious disease among children.