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Simple Summary: Drought is a global climatic phenomenon and one of the main factors that negatively affect plant growth. Karst is a unique type of ecosystem where ecological degradation is becoming more and more serious due to the aggravation of global drought. Vegetation restoration is an effective method for preventing ecological degradation in Karst ecosystems. Cinnamomum migao is selected as the tree species for vegetation restoration, because it is a unique, fast-growing medicinal plant of Southwest China that only thrives in Karst regions. Arbuscular mycorrhizal fungi (AMF) are an important component of the soil biota in ecosystems and alleviate drought stress in plants by forming a mutualistic symbiosis. Most previous studies just considered the effects of AMF species on drought resistance but did not evaluate different inoculation methods. The aim of the present study was to compare the effects of different AMF resulting from the use of different inoculation methods on the growth and drought resistance of C. migao seedlings in Karst soil. The findings of this study will improve the success rate of reforestation programs in Karst ecosystems through the utilization of these important microorganisms. Drought stress is one of the greatest obstacles affecting field crop productivity in arid and semi-arid regions, and its severity and frequency are expected to increase due to human-induced changes to the environment and climate. Drought has led to rocky desertification in Karst regions. Cinnamomum migao is a unique, fast-growing medicinal plant of Southwest China that only thrives in Karst regions. Arbuscular mycorrhizal fungi (AMF) symbiosis alleviates drought stress in plants; however, establishment and function of the symbiotic interaction between AMF host plant in relation to the inoculation method remain unclear. Therefore, we conducted an experiment to investigate the effects of AMF species (Glomus etunicatum and Funneliformis mosseae) and two inoculation methods (seed vs. seedling inoculation) under drought stress on C. migao seedlings, and quantified mycorrhizal colonization, AMF spore density, root vigor, relative water content, C. migao growth, antioxidant enzyme activities, and osmotic adjustment. Inoculation with AMF (G. etunicatum and F. mosseae) positively affected the growth and root vigor of Cinnamomum migao under drought stress, regardless of the inoculation method. Additionally, both AMF species markedly upregulated antioxidant enzyme activities and osmotic adjustment substances, regardless of the inoculation method. Our results showed that the collective stimulatory effect of G. etunicatum is more efficient than that of F. mosseae. AMF application could promote afforestation with C. migao to prevent rocky desertification in Karst regions where water is the greatest limiting factor on plant growth and yield. [ABSTRACT FROM AUTHOR]