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Opisthopappus is a major wild source of Asteraceae with good cold and drought resistance. Two species of this genus (Opisthopappus taihangensis and Opisthopappus longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus revealed a higher expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly regarding monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus, 1203 genes were found that related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Different PSG expressions occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Two PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights as to how the two species adapted to different environments, characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species of Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.