In this experiment, wild-type Artemisia selengensis, Chrysanthemum, Artemisia annua and mugwort were used as rootstocks, while cultivated A. selengensis served as the scion. Cleft grafting was identified as the most effective method. The highest survival rate was observed when wild-type A. selengensis was used as the rootstock, reaching 92.5% on the 12th day post-grafting, with quicker callus formation than in other combinations. The combination of wild-type A. selengensis rootstock and cultivated A. selengensis scion demonstrated the greatest grafting compatibility, whereas the pairing of cultivated A. selengensis with chrysanthemum showed the lowest. During the healing phase, analysis revealed that in compatible graft combinations, soluble sugar levels increased, with a significant rise in soluble protein levels. Following callus formation, levels of superoxide dismutase (SOD), peroxidase (POD), and phenylalanine ammonia-lyase (PAL) declined. Hence, soluble sugars, SOD, POD, and PAL may act as indicators of grafting compatibility in A. selengensis. Weekly elongation measurements from 21 to 49 days post-grafting indicated that combinations rooted in chrysanthemum exhibited markedly greater elongation from 35 to 49 days than other pairs. Comparisons of soluble proteins, sugars, vitamin C, and flavonoids in the scion on days 49, 70, and 91 post-grafting with those in ungrafted plants suggested that different rootstocks differentially influenced nutrient and metabolite accumulation in A. selengensis. These findings suggest that future research could explore the mechanisms underlying these changes during the grafting process. Integrating molecular biology and metabolomics techniques will aid in elucidating specific regulatory mechanisms affected by grafting in Artemisia species, potentially enhancing the content of nutrients or bioactive compounds. This could provide theoretical support for biopharmaceutical applications and propose new methods for improving the quality of Artemisia germplasm resources.