The antifungal activity of carvacrol against food-spoilage yeast Zygosaccharomyces rouxii (Z. rouxii) was studied， and the potential antifungal mechanism was analyzed from the perspective of apoptosis for the first time. The diameter of inhibition zone (DIZ)， minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) were determined by oxford cup method and double dilution method. The morphological changes of Z. rouxii cells were observed by scanning electron microscope. Then， a series of the biochemical and morphological characteristics of typical apoptosis was detected using flow cytometer or microplate reader， and the transcription levels of key apoptosis regulatory factors were measured by qRT-PCR. The DIZ， MIC and MFC of carvacrol against Z. rouxii were (13.67 ± 0.58) mm， 0.156 mg/mL and 0.3125 mg/mL， respectively. The cell surface wrinkled under the MIC and MFC of carvacrol. Under MIC carvacrol treatment， increased intracellular reactive oxygen species level， elevated intracellular Ca2+ concentration， decreased mitochondrial membrane potential， metacaspase activation， phosphatidylserine exposure and DNA fragmentation were observed in Z. rouxii cells. Moreover， the transcription levels of pro-apoptotic factors including Yca1， Dnm1， Cyc1， Nuc1 and Ndi1 were up-regulated by 1-4 fold. Carvacrol seemed to induce Z. rouxii apoptosis through a metacaspase-dependent mitochondrial pathway. The results can provide new insights into the antifungal mechanism of carvacrol， and propose a theoretic basis for the development of green and efficient food preservatives.