Summary Flavones, a key group of flavonoids, play a significant role in plant adaptation to ecological niches and are valuable medicinal resources. However, the genetic basis underlying their contribution to ecological adaptation remains largely unknown. Here, using metabolite‐based genome‐wide association study, we report that the natural variation of flavone contents in Chrysanthemum indicum , a wild chrysanthemum and medicinal herb, is mainly determined by a recently duplicated flavone synthase II gene CiFNSII‐1.2 . Enzymatic assays and molecular dynamics simulations reveal that the key amino acid residues 246 th and 261 th confer the higher enzymatic activity of CiFNSII‐1.2 compared with its ancestral form. These residues act as critical modulators, regulating the flexibility of the external entrance and contributing to the enzyme's improved functionality. Transgenic evaluation demonstrate that CiFNSII‐1.2 contributes to flavone accumulation and drought adaptation. Our findings provide insights into the biochemical and evolutionary role of flavones in facilitating adaptation to drought‐prone habitats in chrysanthemum.