This study was aimed to evaluate the fungicidal effects of oregano essential oil (OEO) fumigation combined with intermediate-wave infrared (IWIR) heating on Aspergillus flavus ( A. flavus ) in peanuts, and investigate the synergistic mechanism of the combined treatment (OEO-IWIR). Vitro experiments results indicated that OEO fumigation completely inhibited the A. flavus mycelium growth and aflatoxin production at a dose of 135 mg/L for 6 h. Meanwhile, the sterilization efficacy was assessed by inoculating peanuts with 6 log 10 CFU/g A. flavus spores. OEO-IWIR exhibited synergistic effects and reached the 5-log reduction requirement by OEO fumigation at 135 mg/L for 6 h combined with IWIR heating at 65 °C for 1 h. Next, cultivability and spore viability tests of A. flavus were assayed. IWIR heating caused culturable sublethal spores, while the OEO-IWIR exhibited complete inactivation. Finally, the mechanism study confirmed that OEO-IWIR caused a higher degree of cell membrane permeabilization (from 17.0% to 65.6%), more significant alteration of cellular ultrastructure, and higher inhibition of ATPase activity than single treatments. • A. flavus cell membrane was the primary antifungal site of OEO fumigation. • OEO-IWIR exhibited a synergistic effect and inactivated 5-log A. flavus spores. • Synergistic effects limited the recovery of sublethal A. flavus spores. • Synergistic effects caused more severe damage to the A. flavus cell membrane.