Little is known about the impact of socio-economic and environmental factors on the associations between PM2.5 exposure and health risk for elementary students. We estimated the space variability of effects of PM2.5 on daily illness-related absence rate for 2278 elementary schools from 97 counties across Jiangsu Province with data collected in the 2016-17 academic year. We evaluated the effects at school- and county-scales and examined the role of socio-economic and environmental factors with generalized addictive models (GAM). With an interquartile range (IQR, 32 μg/m3) increase in PM2.5 concentration, the relative risk of absence rate for a given school ranged between 1.00 and 2.81. Factors including high economic development level, low health expenditure, dense road network, dense population and low vegetation coverage drove strong effects for schools/counties. For the implementation of efficient clean air policies and public health interventions, we should concern about not only high-polluted areas but also areas under specific socio-economic and environmental conditions.