Air pollution addresses short-term health effects on morbidity, especially for children. Assessing the impacts of air pollution on elementary students is critical for developing preparedness response strategies for this sensitive group. In the 2016–17 academic year, up to 687,748 groups of illness-related absence records and the information on whether the absentee had gone to a hospital or not were collected from 2564 elementary schools across Jiangsu Province China. We explored the associations between air pollution and illness-related records using a time-stratified case-crossover analysis with distributed lag non-linear design. An increase of 10 μg/m3 in the current-day concentration of PM2.5 and O3 was positively associated with illness-related absenteeism overall. The excess risk of absenteeism was 4.52 % (95%CI 4.37–4.67 %) for PM2.5 and 0.25 % (95%CI 0.01–0.36 %) for O3. The risk associated with O3 was boosted for the frequent absentees who tended to have basic diseases or were more vulnerable to infectious diseases. Students in 43.1 % illness-related absenteeism, mainly due to highly infectious diseases, only received home nursing without going to a hospital. The increase in the number of illness cases associated with PM2.5 and O3 estimated based on the illness-related absence data was 41.5 % and 18.6 % higher than that evaluated based on hospital visit records. Such underestimations persisted in sensitivity analyses and persisted in subgroups classified by gender or grade. Together, the performance of illness-related absence records far outweighed that of hospital visit data regarding the thorough evaluation of air pollution-related illness cases for elementary students. Improvement in air quality and home health care education are warranted as well for the health benefits of children. Display omitted •Up to 43 % absentees selected home nursing without going to a hospital.•Using hospital visit record undervalued 18–42 % pollution-related illness cases.•PM2.5 exposure was related to increased illness-related absence for all subgroups.•O3 exposure was associated with high absence risk for the less unhealthy group.