The bacteria and fungi captured on heat insulating materials or air filter media in the ventilation system in civil flights may reentrant into the indoor air which poses a threat to passengers' health. The E. coli and B. subtilis bacteria survival rates on the heat insulating blankets typically used as padding materials inside the aircraft walls under the mimicked environmental condition were studied. Then the antibacterial performance of positively charged electret and chitosan modified filter media which can be used in the ventilation systems against E. coli bacteria was investigated. Our results showed that the E. coli survival rate deceased to less than 0.2% and that of the B. subtilis decreased to less than 2.1% of the control samples on the hydrophilic and hydrophobic blankets under the mimic conditions after one flight cycle. The survival rate of E. coli on the positively charged electret filter media decreased to less than 30% compared to the uncharged filter media after six hours due to the disruption of their metabolic balance by the positive charges on the fibers surface. Moreover, the E. coli survival rate on the pure nylon, nylon/chitosan and chitosan dipped nylon-6 nanofibmus filter media decreased to 8.4%, 7.1% and 2.8% after 120 min, respectively. This study sheds light on fabrication of the eco-friendly antibacterial filter materials for the ventilation systems.