In recent years, deoxynivalenol (DON) has frequently been detected in wheat grains and their products. The enantioselective impact of flutriafol on the growth and DON biosynthesis of Fusarium graminearum was investigated in relation to water activity (αw, 0.97 and 0.99) and temperature (20, 25, and 30 °C) on the wheat-based medium. R-(-)-flutriafol exhibited higher bioactivity than S-(+)-flutriafol and Rac-flutriafol under the above conditions. Flutriafol enantiomers reduced or stimulated DON biosynthesis depending on αw. DON levels were negligible after 14 or 7 days of incubation times under 0.97 and 0.99 aw, respectively. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses showed that the expression levels of trichothecene biosynthetic (TRI) genes of F. graminearum under 0.97 aw were significantly higher than those under 0.99 aw. In addition, R-(-)-flutriafol can induce more TRI gene expression than S-(+)-flutriafol. Taken together, this study indicated that aw and temperature play important roles in regulating DON biosynthesis in F. graminearum with flutriafol enantiomers.