Various metabolic processes are activated in response to environmental changes. Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. We investigated whether these aromatics might be differentiated and inherently adaptive attributes. To determine the potential differentiation and environmental response patterns between O. longilobus and O. taihangensis, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus reciprocal transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles between O. longilobus and O. taihangensis flowers were observed, and 29 substances related to their scents were obtained (two alkenes, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids) of which eugenol and chlorogenic were the primary aromatictic molecules. The chlorogenic content of TH was significantly higher than that of CLW and CLT, while the eugenol content was highest in CLT followed by TH, and both metabolites were enriched in the phenylpropane pathway. In addition, the aromatic related compounds were significantly correlated with the lowest temperatures in October and in December. The results above indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.