In order to solve the problem of infestation of fresh fruit after making them into candied fruit and the quality degradation caused by the infestation, a combined ozone-microwave sterilization method was used to treat four candied fruit molds.Response surface optimization analysis showed that when the ozone infusion time was at 10 min and with 560 W microwave power for 20 s, the inhibition rates of the four candied fruit molds S1, S2, X1, and H1 were 100%, 94.28%, 100%, and 100%, respectively. Moreover, according to the characterization of morphology, DNA electrophoretic profiles, and nucleic acid/protein leakage test, the integrity of the mold cell membrane was destroyed after the combined ozone-microwave treatment because of the thermal and nonthermal effects of microwave and the strongly oxidizing properties of ozone. The molds were dead because of the efflux of intracellular nucleic acid and protein and the degradation of DNA, which influenced normal cellular metabolism. Quality identification showed a better expected quality of candied fruit.