This study was conducted to help manage total floating bacteria and fungi in the indoor air by studying the characteristics of total floating bacteria and fungi according to the indoor CO2 concentration of daycare centers. The sampling and analysis of samples was based on the indoor air quality process test method, and the result analysis was conducted using the SPSS statistical program to perform correlation and regression analysis. Correlation and regression results show that CO2 and total airborne bacteria showed positive relationships, but airborne mold did not show relevance. In addition, in order to identify factors affecting airborne mold, correlation analysis and regression analysis were performed regarding total airborne bacteria, PM10, PM2.5, HCHO, outdoor mold, I/O ratio, indoor temperature/ humidity, area per classroom and volume. The results showed that the factors affecting airborne mold were I/O ratio, outdoor airborne mold, and total airborne bacteria. Research results show that CO2 and total airborne bacteria can be reduced and controlled by natural ventilation, and in the case of airborne mold, mechanical forced ventilation such as hoods will be necessary due to the introduction of outdoor airborne mold. In addition, it is necessary to consider I/O ratio criteria in order to confirm effective indoor mold contamination, taking into account the effect of outdoor mold inflow.