Dark septate endophytes (DSEs) can improve the performance of host plants grown in heavy metal-polluted soils, but the mechanism is still unclear. A sand culture experiment was performed to investigate the effects of a DSE strain (Exophiala pisciphila) on maize growth, root morphology, and cadmium (Cd) uptake under Cd stress at different concentrations (0, 5, 10, and 20 mg·kg−1). The results indicated that the DSE significantly improved the Cd tolerance of maize, causing increases in biomass, plant height, and root morphology (length, tips, branch, and crossing number); enhancing the Cd retention in roots with a decrease in the transfer coefficient of Cd in maize plants; and increasing the Cd proportion in the cell wall by 16.0–25.6%. In addition, DSE significantly changed the chemical forms of Cd in maize roots, resulting in decreases in the proportions of pectates and protein-integrated Cd by 15.6–32.4%, but an increase in the proportion of insoluble phosphate Cd by 33.3–83.3%. The correlation analysis revealed a significantly positive relationship between the root morphology and the proportions of insoluble phosphate Cd and Cd in the cell wall. Therefore, the DSE improved the Cd tolerance of plants both by modifying root morphology, and by promoting Cd binding to the cell walls and forming an insoluble phosphate Cd of lower activity. These results of this study provide comprehensive evidence for the mechanisms by which DSE colonization enhances Cd tolerance in maize in root morphology with Cd subcellular distribution and chemical forms.