In addition to usual concerns about mold-induced deterioration, the potential impacts of bacteria in cultural relic preservation and exhibition environments have received more and more attention. Removal or reduction of airborne microorganisms inside museum exhibition halls would be helpful to preserve cultural relics. In our study, five plant-derived extracts were used as purifying agents to fumigate, in the plate, airborne microorganisms sampled from a museum exhibition hall. In order to evaluate the effects of inhibition on airborne microorganisms, the bacteria were quantified by pure culture method, and the bacterial compositions were characterized by the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique. The results show that citral had the best bacteriostatic effect and the weakest one was geranium oil. After fumigation with high doses of citral, citronellol and linalool, the total bacterial colonies were found decline by 98.53%, 98.53% and 97.95%, respectively. As a result, the richness and diversity index of airborne bacteria also declined significantly. In addition, the PCR-DGGE profile indicates that citral and citronellol might further improve the antibacterial effect. Our study has demonstrated that, as a kind of purifying agent for airborne microorganisms, plant-derived extracts have good prospects for decontamination of museum exhibition halls.