Conyza blinin (C. blinii) is a traditional Chinese medicine plant grown in Sichuan, China. C. blinii is suitable for studying the tolerance mechanism of plants to iron because of its high iron content. Our results show that the growth and development of C. blinii is improved under iron at a specific concentration. Iron increased the content of endogenous auxin in C. blinii, improving the glandular trichome (GT) density and the content of blinin, the characteristic diterpene in C. blinii, which may enhance its tolerance to iron stress. We used RNA sequencing analysis to explore the differential gene transcription in C. blinii under iron stress to provide a reference for the study of other iron-sensitive plants. The results showed that most of the key enzymes in the blinin synthesis pathway were upregulated under iron stress. In addition, the process by which C. blinii responds to iron stress through IAA may be related to CbHO-1. Taken together, these results suggest that the increase in GT density and auxin-mediated blinin content improve the growth of C. blinii under iron stress.