Chrysanthemum morifolium cv. Fubaiju, a traditional tea in southern China with high nutritional and health functions was used in this study. Optimized production conditions of a novel chrysanthemum rice wine (FRW) were obtained by the Box–Behnken design response surface experiment. FRW with best sensory quality was developed with 0.68% chrysanthemum, 0.79% Jiuqu and 0.81:1 liquid‐to‐solid ratio. Compared with rice wine (RW) control, the total phenolic and flavonoid contents, as well as antioxidant activity of the FRW increased significantly. GC–MS analysis showed that more flavor compounds including alcohols, aldehydes, acids, and esters were detected in FRW. During the aging process, it was found that the antioxidant substances, the antioxidant activity and the flavor substances decreased, with the wine body tending to be homogenized. After 6 months of storage, overall sensory quality of FRW was more harmonious, with special nectar taste, which dramatically improved the flavor characteristics and functionality compared with traditional RW.