Drought severely impacts plant growth, inducing oxidative stress. Although methyl jasmonate (MeJA) mitigates drought effects in many plants, its physiological mechanism in medicinal Chrysanthemum morifolium remains unclear. We used different concentrations (0.1, 1, 10, 100, 1000 mg L-1) of methyl jasmonate (MeJA) on foliage to explore whether exogenous MeJA can improve the drought resistance of medicinal C. morifolium by affecting the growth and physiological characteristics, and to determine a suitable exogenous MeJA concentration. Results showed that with the prolongation of drought stress, plant height, crown width, leaf area and leaf thickness of the two species of medicinal C. morifolium in the seedling stage first increased and then decreased, the green leaf rate gradually decreased, the above-ground and below-ground dry weights increased, the relative water content (RWC) of leaves decreased, the relative chlorophyll content (SPAD) firstly increased and then decreased, the content of MDA increased, and the activities of antioxidant enzymes (SOD, POD and CAT) all increased before being followed by a decrease. Our comprehensive evaluation analysis by the affiliation function concluded that it was more effective to treat 'Huaibaiju' with 10 mg L-1 MeJA and 'Wuyuanhuangju' with 1 mg L-1 MeJA, which could effectively alleviate the damage caused by drought stress. The study provides insights into the potential application of MeJA in enhancing the resilience of medicinal plants under drought stress, which could contribute to the sustainable cultivation of medicinal C. morifolium in arid regions.