Greater attention is currently being paid to the relationship between indoor environment and childhood allergies, however, the lack of reliable data and the disparity among different areas hinders reliable assessment of the relationship. This study focuses on the effect of indoor pollution on Chinese schoolchildren and the relationship between specific household and health problems suffered. The epidemiological questionnaire survey and the field measurement of the indoor thermal environment and primary air pollutants including CO₂, fine particulate matter (PM_2.5), chemical pollutants and fungi were performed in six Chinese cities. A total of 912 questionnaires were eligible for statistical analyses and sixty houses with schoolchildren aged 9–12 were selected for field investigation. Compared with Chinese national standards, inappropriate indoor relative humidity (70%), CO₂ concentration exceeding 1000 ppm and high PM_2.5 levels were found in some monitored houses. Di(2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) were the most frequently detected semi-volatile organic compounds (SVOCs) in house dust. Cladosporium, Aspergillus and Penicillium were detected in both indoor air and house dust. This study indicates that a thermal environment with CO₂ exceeding 1000 ppm, DEHP and DBP exceeding 1000 μg/g, and high level of PM_2.5, Cladosporium, Aspergillus and Penicillium increases the risk of children’s allergies.