In order to investigate the effect of rice wine processing on the residue of the chiral pesticide hexaconazole and evaluate its health risk, samples were collected at different stages of rice wine processing (paddy, rice hulls, brown rice, polished rice, soaked rice, cooked rice, and rice wine) and the residue levels of hexaconazole enantiomers in these samples were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Risk assessment models were used to evaluate the risk of dietary exposure to hexaconazole enantiomers. The results showed that the recoveries of (+)-hexaconazole and (-)-hexaconazole spiked into the seven samples were in the range of 88.2%–105.7% and 85.3%–104.3% with relative standard deviations (RSD) of 0.8%–8.3% and 0.6%–9.6%, respectively. The processes of dehulling, aleurone layer removal, washing, soaking, and cooking all significantly reduced hexaconazole residues, and the contents of (+)-hexaconazole and (-)-hexaconazole reduced from 10.64 and 10.10 to 0.13 mg/kg with processing factor (PF) of 0.94, 0.45, 0.06, 0.50 and 0.93, 0.41, 0.06, 0.52, respectively and enantiomeric fraction (EF) values of about 0.5, indicating that the concentration of hexaconazole gradually reduced during the processing of rice wine with no significant differences being observed between the two enantiomers. However, during the fermentation process, the contents of (+)-hexaconazole and (-)-hexaconazole increased selectively from 0.13 to 0.80 and 0.66 mg/kg with PF > 1 and EF value of 0.55, respectively. This indicated that the fermentation process of rice wine selectively increased the content of hexazolol, and the content of (+)-hexazolol was greater than that of (-)-hexazolol. The dietary risk assessment results showed that the chronic risk quotients (CRQ) of (+)-hexaconazole and (-)-hexaconazole in paddy and brown rice were both greater than 100%, which decreased to acceptable levels of 6.2% and 5.2%, respectively after aleurone layer removal. The results of this study provide a basis for the dietary risk assessment of the chiral pesticide hexaconazole in rice wine processing.