Indoor environment is critical in health and disease, where “Sick building syndrome” is the result of poor indoor air quality. Fungal spores are major biological suspended particles in the air that affect allergy sufferers through respiratory infections and skin exposure. Atopic dermatitis (AD) is the most common skin allergic symptom, but the airborne fungi that cause AD are not clear. The purpose of this study was to reduce indoor air pollutants and fungal antigens/allergens in the living space of two AD cases with active disease through the analysis of the composition of airborne fungi and the improvement of indoor air quality with both engineering and behavioral interventions by, in part, improving the indoor ventilation systems. We tracked changes in fungal community and compared health indicators of two cases. After interventions, fungal total counts in the air of subjects’ bedrooms decreased from 10⁴-10⁵ spores/m³ to 10³-10⁴ spores/m³, the culturable counts decreased from 310-490 CFU/m³ to 23-156 CFU/m³. The most dominant fungi, including Penicillium, Aspergillus, Cladosporium, and Sarocladium, in the bedroom were all decreased, while the concentrations of monocyte chemoattractant protein-1 (MCP-1) in the serum of two subjects were decreased from 116 and 118 pg/ml to 62 and 83 pg/ml, respectively, two-three months after intervention. The severity of AD in one subject was improved as evidenced by the reduction of EASI score, which was decreased from 13.5 to 9.2. These results suggest that the intervention effectively reduced indoor air fungal concentrations and improved the inflammatory responses in subjects with AD.