Pinus massoniana (Massion’s pine), a pioneer tree species, exhibits restoration potential in polluted mining areas. However, the physiological and molecular mechanisms of ectomycorrhizal (ECM) fungi in Massion’s pine adaptability to multiple-toxic-metal stress are still unclear. Hence, Massion’s pine seedlings inoculated with two strains of C. geophilum, which were screened and isolated from a polluted mine area, were cultivated in mine soil for 90 days to investigate the roles of EMF in mediating toxic metal tolerance in host plants. The results showed that compared with the non-inoculation control, C. geophilum (CG1 and CG2) significantly promoted the biomass, root morphology, element absorption, photosynthetic characteristics, antioxidant enzyme activities (CAT, POD, and SOD), and proline content of Massion’s pine seedlings in mine soil. C. geophilum increased the concentrations of Cr, Cd, Pb, and Mn in the roots of Massion’s pine seedlings, with CG1 significantly increasing the concentrations of Pb and Mn by 246% and 162% and CG2 significantly increasing the concentrations of Cr and Pb by 102% and 78%. In contrast, C. geophilum reduced the concentrations of Cr, Cd, Pb, and Mn in the shoots by 14%, 33%, 27%, and 14% on average, respectively. In addition, C. geophilum significantly reduced the transfer factor (TF) of Cr, Cd, Pb, and Mn by 32–58%, 17–26%, 68–75%, and 18–64%, respectively, and the bio-concentration factor (BF) of Cd by 39–71%. Comparative transcriptomic analysis demonstrated that the differently expressed genes (DEGs) were mainly encoding functions involved in “transmembrane transport”, “ion transport”, “oxidation reduction process”, “oxidative phosphorylation”, “carbon metabolism”, “glycolysis/gluconeogenesis”, “photosynthesis”, and “biosynthesis of amino acids.” These results indicate that C. geophilum is able to mitigate toxic metals stress by promoting nutrient uptake, photosynthesis, and plant growth, thereby modulating the antioxidant system to reduce oxidative stress and reducing the transport and enrichment of toxic metals from the root to the shoot of Massion’s pine seedlings.