A growing number of studies have shown that the indoor residential environment is associated with respiratory and allergic diseases in children. This study aimed to investigate the prevalence of respiratory and allergic diseases among children in China and its correlation with using air handling equipment, based on the cross-sectional survey results of the China Children Homes Health Project in 2010 and 2019. The binary logistic regression model was used to explore the association between asthma, rhinitis, eczema and pneumonia and the use of air handling equipment in children. The prevalence of children’s respiratory and allergic diseases has decreased, and the usage rate of portable air purifiers and split air conditioners has increased in 2019 compared to 2010. The results showed that using a fresh air system with filters was negatively correlated with children’s pneumonia (adjusted odds ratio (aOR): 0.767, 95% confidence interval (95% CI): 0.704–0.835). The use of portable air purifiers was positively correlated with most diseases’ symptoms in two undertaken surveys. In 2019, the positive correlation between using split air conditioners and asthma-related symptoms decreased compared with 2010, while it was positively correlated with rhinitis, eczema and pneumonia. To avoid children’s allergic diseases and reduce respiratory symptoms, parents should choose appropriate air handling equipment.