Terpenoids are important secondary metabolites in plants. The synthesis of terpenoids involves a key enzyme, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR). In an aromatic ornamental plant, Chrysanthemum indicum var. aromaticum, terpenoids were found to be an important component in leaf secretions. To study the regulatory mechanism of terpenoid synthesis in C. indicum var. aromaticum, we cloned the DXR gene from C. indicum var. aromaticum, named CiDXR, based on transcriptome data. CiDXR is 1419 bp, encoding a polypeptide chain of 472 amino acids. Comparative and bioinformatic analysis showed that CiDXR was highly similar to DXRs from other plant species. The protein product of CiDXR was analyzed for physical and chemical properties, and secondary and tertiary structures. Methyl jasmonate (MeJA) is an effective exogenous elicitor that can impact the synthesis of secondary metabolites by regulating the expression of a series of specific key enzymes. In our study, MeJA treatment was used to study the relationship between CiDXR expression and terpenoid metabolism. The expression pattern of CiDXR was analyzed by quantitative real-time polymerase chain reaction. Leaves expressed the highest level of CiDXR mRNA. In addition, CiDXR expression was found to be activated by MeJA, up to 20-fold at 24 h post induction. The MeJA treatment significantly affected the relative contents of the secretion products, and the induction effect was maximal at 24 h, consistent with the expression of CiDXR. This study shows that CiDXR may play a key regulatory role in the control of terpenoid synthesis in C. indicum var. aromaticum.