Salvia miltiorrhiza (S. miltiorrhiza) Bunge is one of the most economically important medicinal crops in China. In traditional Chinese medicine, its root is used as an important ingredient in formulas for treatment of atherosclerosis-related disorders. The continuous cropping of S. miltiorrhiza increases the proportion of dried seedlings and decreases the biomass of the shoots and roots and the contents of active components. In this study, three field experiments were conducted to investigate the effects of Glomus mosseae (G. mosseae) inoculation on the growth and contents of active ingredients and nutrients in continuously cropped S. miltiorrhiza. The results showed that inoculation with G. mosseae increased the shoot biomass of S. miltiorrhiza by 48.1% and the root biomass by 39.2%, and decreased the dried seedling rate by nearly 75%. Inoculation with G. mosseae also increased the salvianolic acid B concentration by 21.9% in the shoots and 9.2% in the roots of S. miltiorrhiza, and also significantly increased Mn concentration in the roots and shoots (by 65.1% and 93.4%, respectively) and Fe concentration in the roots (by 75%). The accumulation of salvianolic acid B, Mn, and Fe in G. mosseae inoculated S. miltiorrhiza may be a mechanism that imparts tolerance to continuous cropping. Inoculation of S. miltiorrhiza with G. mosseae can serve as an effective approach of biocontrol to improve the performance of continuously cropped S. miltiorrhiza.