Heavy metals can adversely affect the growth and metabolic processes of plant. Arbuscular mycorrhizal (AM) fungi, which colonize the roots of most plants, may change the uptake and resistance to heavy metals by altering plant metabolism. But few published papers focused on how AM fungi enhanced plant tolerance to heavy metals at the metabolomics level. Therefore, our study incorporated LC-MS technology to explore the molecular mechanism by which AM fungi improved cadmium (Cd) tolerance of Bahia grass (Paspalum notatum) at the metabolomic scale. The results showed that AM fungi increased growth of Bahia grass, and enhanced its uptake and tolerance of Cd. Infection with AM fungi significantly raised the levels of both primary metabolites (amino acid, carbohydrate, organic acid, etc.) and secondary metabolites (such as terpenoids, phenolic compounds, and alkaloids), which in turn improved the photosynthesis efficiency, osmoregulation, and antioxidation defense of the plant, thereby enhancing the Cd tolerance of Bahia grass. Furthermore, under high concentration of Cd, both TCA cycle and lipid metabolism were generally suppressed, and AM fungi inoculation alleviated the effects and normalized the TCA cycle and lipid metabolism. In all, the metabolic alterations identified here provided insights into the mechanisms by which AM fungi enhanced plant tolerance to heavy metals.