<p>This study evaluated the efficacy of five physical technologies, including catalytic infrared (CIR), radiofrequency (RF), pulsed light (PL), low-temperature plasma (LTP), and ozone (O₃), for inactivating aflatoxigenic <i>Aspergillus flavus</i> (<i>A. flavus</i>) in rice. Individually, these treatments showed limited antimicrobial activity, with ozone performing the highest efficacy among single treatments (<i>p</i> &lt; 0.05). Combining treatments produced synergistic effects: CIR or RF with PL or LTP significantly reduced microbial counts by 1.0—3.0 log (<i>p</i> &lt; 0.05), whereas integrating ozone with tempering (60℃, 240 min) achieved effective antifungal activity and shortened the required exposure time. The sequence of treatments showed no significant effect. Mechanistic analysis revealed that both thermal and non-thermal effects disrupted spore cell walls and membranes, significantly increasing electrolyte leakage (<i>p</i> &lt; 0.05). Microscopic images showed structural collapse and perforation under combined treatments. Rice quality was largely maintained. Thermal treatments significantly improved head rice yield (HRY) (from 52.3% to 60.6%) (<i>p</i> &lt; 0.05) through moisture migration, while ozone treatment decreased amylose content (AC) from 16.93% to 14.83% (<i>p</i> &lt; 0.05). Heat retention mitigated these effects and balanced quality parameters. Overall, combining physical technologies with controlled tempering significantly enhances <i>A. flavus</i> inactivation while preserving rice quality. These findings demonstrate a feasible, non-chemical strategy for enhancing fungal safety in rice while maintaining processing quality.</p> Graphical Abstract <p></p>