The incidence of halitosis has a prevalence of 22-50% throughout the world and is generally caused by anaerobic oral microorganisms, such as Fusobacterium nucleatum, Clostridium perfringens, and Porphyromonas gingivalis. Previous investigations on the structure-activity relationships of ginsenosides have led to contrasting results. Particularly, the antibacterial activity of less polar ginsenosides against halitosis-related bacteria has not been reported. Crude saponins extracted from the Panax quinquefolius leaf-stem (AGS) were treated at 130°C for 3 h to obtain heat-transformed saponins (HTS). Five ginsenoside-enriched fractions (HTS-1, HTS-2, HTS-3, HTS-4, and HTS-5) and less polar ginsenosides were separated by HP-20 resin absorption and HPLC, and the antimicrobial activity and mechanism were investigated. HPLC with diode-array detection analysis revealed that heat treatment induced an extensive conversion of polar ginsenosides (-Rg1/Re, -Rc, -Rb2, and -Rd) to less polar compounds (-Rg2, -Rg3, -Rg6, -F4, -Rg5, and -Rk1). The antimicrobial assays showed that HTS, HTS-3, and HTS-4 were effective at inhibiting the growth of F. nucleatum, C. perfringens, and P. gingivalis. Ginsenosides-Rg5 showed the best antimicrobial activity against the three bacteria, with the lowest values of minimum inhibitory concentration and minimum bactericidal concentration. One major reason for this result is that less polar ginsenosides can more easily damage membrane integrity. The results indicated that the less polar ginsenoside-enriched fraction from heat transformation can be used as an antibacterial agent to control halitosis.